PRGDB00049679 (gag/pol)

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gag/pol
Gene Type Putative_R-Genes,_collected_from_NCBI_Protein
GenBank 2586078 (U72726)
Gene Class Unknown
Domain Type
Gene Species Oryza longistaminata

Comment?

Oryza longistaminata receptor kinase-like protein, family member D, and retrofit (gag/pol) genes, complete cds.

DNA Sequence

ATGGCGTCGTCGTCGTCTTCCTCAGGCGCGGCAGCCGCCAATCTCCTCCAAGGCCACTCGGTTTCAGAGAAACTCGGGAAAGCCAACCATGCATTGTGGAAAGCGCAAGTTAGCGCTGCAGTGCGTGGAGCCCGATTGCTGGGCTACCTCAACGGCGATATCAAAGCTCCAGACGCCGAACTCTCGGTCACCATAGATGGGAAGACCACAACAAAGCCGAATCCGGCATTTGAAGATTGGGAGGCCAATGACCAGCTTGTTCTTGGCTATCTCCTGTCATCTCTTTCAAGGGATGTGCTGATCCAAGTCGCCACATGCAAGACGGCGGCTGAGGCATGGCGGAGCATTGAAGCACTCTACTCCACCGGCACTCGAGCAAGGGCGGTGAACACCAGACTCGCCCTCACCAACACGAAGAAAGGAACAATGAAGATCGCCGAGTATGTCGCCAAGATGCGAGCGCTTGGTGATGAGATGGCTGCCGGCGGTCATCCACTTGATGAAGAAGACCTTGTCCAGTACATCATCGCTGGGCTAAATGAAGACTTCAGCCCGATCGTCTCCAACCTCTGCAACAAGTCCGATCCCATCACGGTTGGGGAGCTGTATTCTCAGCTCGTCAACTTTGAAACCCTCCTTGATCTCTACCGCAGCACTGGTCAGGGAGGAGCTGCTTTTGTCGCTAATCGCGGCAGGGGCGGCGGCGGCGGCGGGCGCGGCAACAACAACAACTCCGGCGGCGGCGGCGGCAGAAGCGCGCCGGGTGGACGCGGCAGCGGCAGCCAGGGTCGCGGTGGCCGTGGACGCGGCACAGGAGGCCAAGACAGGCGCCCTACTTGCCAAGTTTGTTTCAAGCGTGGGCATACAGCAGCTGATTGTTGGTATCGCTTCGACGAGGACTACGTTGCAGATGAGAAGCTCGTTGCTGCTGCTACTAACTCGTATGGTATAGATACAAATTGGTATATTGATACAGGTGCTACAGATCACATTACCGGTGAACTAGAGAAGCTTACCACCAAGGAGAAATACAACGGCGGCGAGCAAATTCACACTGCTAGCGGAGCAGGTATGGATATTAGTCACATTGGTCATACTATTGTGCATACCCCTAGCCGTAATATTCATCTAAATAATGTCCTTTATGTTCCTCAAGCCAAGAAAAATCTTATATCTGCTAGTCAATTAGCCGCTGATAATTCTGCTTTTCTTGAACTTCACTCGAAATTCTTTTCTATAAAGGATCAGGTAACGAGGGACGTTCTGCTTGAAGGGAAATGTAGACACGGTCTCTACCCGATCCCCAAGTTCTTTGGTCGCTCAACCAACAAACAAGCCCTTGGTGCCGCCAAGTTATCCCTGTCTAGGTGGCATAGCCGTCTAGGACATCCGTCTCTTCCTATTGTTAAGCAAGTCATTAGCAGAAATAATCTCCCATGTTCAGTTGAGTCAGTCAATCAGTCTGTGTGTAATGCTTGCCAAGAAGCAAAGAGTCATCAGTTACCTTATATTAGATCTACTAGTGTGTCTCAATTTCCTCTTGAACTTGTTTTTTCTGATGTTTGGGGCCCTGCTCCAGAGTCTGTTGGGAGAAATAAATATTATGTGAGTTTCATTGATGATTTTAGTAAGTTTACTTGGATATACTTGCTGAAATACAAGTCTGAGGTTTTTGAGAAATTTAAAGAATTTCAGGCTTTAGTTGAACGAATGTTTGATAGAAAGATTATTGCCATGCAGACTGATTGGCGGGGGGGGAGATATCAGAAACTTAATTCCTTTTTTGCTCAAATAGGATTGATCATCATGTGTCATGTCCTCACACTCATCAGGCAGAATGGGTCAGCTGAGAGAAAACACCGGCATATCGTGGAAGTAGGCCTTTCTCTTTTATCTTATGCATCAATGCCTCTTAAGTTTTGGGATGAAGCCTTTGTTGCAGCCACTTATCTCATCAATCGTATACCTAGTAAAACCATCCAAAATTCTACACCCCTAGAGAAACTGTTTAACCAAAAACCTGACTACTCATCCTTGAGAGTGTTTGGTTGTGCATGTTGGCCTCATCTTCGCCCTTACAATACACACAAACTCCAGTTTCGCTCCAAACAGTGCGTGTTTTTGGGTTTTAGTACTCACCACAAAGGATTTAAGTGTCTTGATGTGTCATCAGGCCGTGTCTACATCTCAAGAGATGTTGTCTTTGATGAAAATGTTTTTCCCTTCTCTACACTCCACTCAAATGCAGGAGCCAGACTCAGGTCTGAAATTCTTTTGTTGCCGTCCCCCTTGACAAACTATAATACGGCTAGTGCAGGGGGAACACATGTAGTTGCACCAGTGGCTAATACTCCATTACCTAGTGATAATTTAATTTCTAATGCTGCTGATGTGACTTCTGGAGAAAATAGTGCAGCACATGAACAGGAAATGGAGAATGAGCAGGAAATAGAGAACGTCATGCATGGGAACGACGTGCATGGGGACGCGGCATCGGGACCTGTGCTGGATCAACCAACTGCTGACAGCAGCACTGCGCCGGACCAGGGAGCTGACACCAGTGACGCGGTCTCTGGCGCAGCTTCTGACGCGGGTGGAGACACTGCCACCCTGGGAGCTGGAGCAGCAAATAGCGCAGCAGCAGGTGGTGAAGAATCCCAGCCGGTGCAGCCTGATGTGACGGGTACAGTACTGGCTACAGTAGCCCCTGCATCGAGACCACACACTCGTCTGCGGAGTGGTATTCGAAAAGAGAAGGTATACACTGATGGCACCGTTAAATATGGTTGTTTTTCTTCTACTGGTGAACCACAAAATGATAAAGAGGCTTTAGGAGATAAAAACTGGAGAGATGCAATGGAAACTGAGTATAATGCTTTGATAAAAAATGACACATGGCACCTAGTTCCATATGAGAAAGGACAAAATATCATTGGGTGTAAATGGGTATATAAGATTAAAAGGAAGGCAGATGGGACACTTGATAGATACAAAGCTAGACTTGTAGCAAAGGGGTTTAAACAAAGATATGGTATCGATTATGAAGATACTTTTAGTCCTGTTGTTAAAGCTGCTACTATTAGAATTATTCTGTCCATTGCTGTCTCTAGAGGTTGGAGTCTTAGACAGTTAGATGTTCAGAATGCCTTTCTTCATGGATTCTTAGAAGAAGAAGTCTACATGCAACAACCTCCTGGGTTTGAGTCATCCTCTAAACCTGATTATGTATGTAAATTGGATAAGGCATTATATGGGCTGAAACAAGCACCAAGGGCGTGGTATTCCAGGCTGAGTAAGAAACTTGTTGAACTTGGTTTTGAAGCTTCAAAGGCTGATACCTCATTATTCTTTCTTAACAAAGGAGGGATACTTATGTTTGTTTTGGTATATGTTGATGATATAATTGTAGCTAGCTCTACAGAGAAGGCAACTACAGCACTTCTGAAGGATCTAAACAAGGAGTTCGCACTTAAGGATTTGGGAGACCTGCACTACTTCCTTGGAATTGAGGTAACTAAAGTTTCCAATGGCGTTATCTTGACTCAAGAGAAGTATGCAAATGATCTGCTAAAGAGAGTTAATATGTCAAATTGCAAGCCAGTTAGTACTCCTCTTTCTGTTAGTGAAAAATTAACTCTATATGAGGGATCACCCTTGGGTCCTAATGATGCAATACAATATAGAAGTATAGTTGGTGCTTTACAATACTTGACCTTGACAAGACCTGACATAGCTTATTCAGTAAACAAAGTCTGTCAGTTTCTTCATGCTCCTACTACCAGTCATTGGATTGCAGTAAAAAGAATCCTCAGATACTTGAACCAATGCACAAGTCTAGGACTTCATATACACAAGAGTGCTTCTACTCTTGTTCATGGGTATTCTGATGCAGACTGGGCAGGTAGTATAGATGACAGAAAATCAACAGGAGGATTTGCAGTATTTTTGGGTTCTAATCTTGTGTCCTGGAGTGCTAGGAAACAACCTACTGTGTCAAGGTCAAGCACAGAGGCAGAATATAAGGCTGTGGCAAATACTACAGCCGAACTGATATGGGTACAAACCTTGTTAAAAGAATTGGGAATTGAGTCTCCTAAAGCTGCCAAGATTTGGTGTGATAACTTAGGAGCTAAATATTTATCAGCTAATCCTGTGTTTCATGCAAGGACAAAGCATATAGAGGTTGATTATCATTTTGTAAGAGAACGAGTGTCACAGAAGCTGTTAGAGATTGATTTTGTTCCATCAGGAGACCAAGTTGCTGACGGGTTTACAAAGGCACTGTCAGCTTGTCTTCTTGAAAATTTTAAACACAATCTTAACCTAGCTAGGTTATGA


Protein sequences

Name Description Sequence
retrofit retrofit [Oryza longistaminata].

MASSSSSSGAAAANLLQGHSVSEKLGKANHALWKAQVSAAVRGARLLGYLNGDIKAPDAELSVTIDGKTTTKPNPAFEDWEANDQLVLGYLLSSLSRDVLIQVATCKTAAEAWRSIEALYSTGTRARAVNTRLALTNTKKGTMKIAEYVAKMRALGDEMAAGGHPLDEEDLVQYIIAGLNEDFSPIVSNLCNKSDPITVGELYSQLVNFETLLDLYRSTGQGGAAFVANRGRGGGGGGRGNNNNSGGGGGRSAPGGRGSGSQGRGGRGRGTGGQDRRPTCQVCFKRGHTAADCWYRFDEDYVADEKLVAAATNSYGIDTNWYIDTGATDHITGELEKLTTKEKYNGGEQIHTASGAGMDISHIGHTIVHTPSRNIHLNNVLYVPQAKKNLISASQLAADNSAFLELHSKFFSIKDQVTRDVLLEGKCRHGLYPIPKFFGRSTNKQALGAAKLSLSRWHSRLGHPSLPIVKQVISRNNLPCSVESVNQSVCNACQEAKSHQLPYIRSTSVSQFPLELVFSDVWGPAPESVGRNKYYVSFIDDFSKFTWIYLLKYKSEVFEKFKEFQALVERMFDRKIIAMQTDWRGGRYQKLNSFFAQIGLIIMCHVLTLIRQNGSAERKHRHIVEVGLSLLSYASMPLKFWDEAFVAATYLINRIPSKTIQNSTPLEKLFNQKPDYSSLRVFGCACWPHLRPYNTHKLQFRSKQCVFLGFSTHHKGFKCLDVSSGRVYISRDVVFDENVFPFSTLHSNAGARLRSEILLLPSPLTNYNTASAGGTHVVAPVANTPLPSDNLISNAADVTSGENSAAHEQEMENEQEIENVMHGNDVHGDAASGPVLDQPTADSSTAPDQGADTSDAVSGAASDAGGDTATLGAGAANSAAAGGEESQPVQPDVTGTVLATVAPASRPHTRLRSGIRKEKVYTDGTVKYGCFSSTGEPQNDKEALGDKNWRDAMETEYNALIKNDTWHLVPYEKGQNIIGCKWVYKIKRKADGTLDRYKARLVAKGFKQRYGIDYEDTFSPVVKAATIRIILSIAVSRGWSLRQLDVQNAFLHGFLEEEVYMQQPPGFESSSKPDYVCKLDKALYGLKQAPRAWYSRLSKKLVELGFEASKADTSLFFLNKGGILMFVLVYVDDIIVASSTEKATTALLKDLNKEFALKDLGDLHYFLGIEVTKVSNGVILTQEKYANDLLKRVNMSNCKPVSTPLSVSEKLTLYEGSPLGPNDAIQYRSIVGALQYLTLTRPDIAYSVNKVCQFLHAPTTSHWIAVKRILRYLNQCTSLGLHIHKSASTLVHGYSDADWAGSIDDRKSTGGFAVFLGSNLVSWSARKQPTVSRSSTEAEYKAVANTTAELIWVQTLLKELGIESPKAAKIWCDNLGAKYLSANPVFHARTKHIEVDYHFVRERVSQKLLEIDFVPSGDQVADGFTKALSACLLENFKHNLNLARL

Domains

Domain Start-End Description Sequence

HMMPfam: PF14244
21-158 UBN2_3,gag-polypeptide of LTR copia-type

VSEKLGKANHALWKAQVSAAVRGARLLGYLNGDIKAPDAELSVTIDGKTTTKPNPAFEDWEANDQLVLGYLLSSLSRDVLIQVATCKTAAEAWRSIEALYSTGTRARAVNTRLALTNTKKGTMKIAEYVAKMRALGDE

HMMSmart: SM00343
IPR001878
279-295 ZnF_C2HC
Zinc finger, CCHC-type

TCQVCFKRGHTAADCWY

HMMPfam: PF13976
442-498 gag_pre-integrs,GAG-pre-integrase domain

TNKQALGAAKLSLSRWHSRLGHPSLPIVKQVISRNNLPCSVESVNQSVCNACQEAKS

superfamily: SSF53098
IPR012337
506-673 RNaseH_fold
Ribonuclease H-like domain

STSVSQFPLELVFSDVWGPAPESVGRNKYYVSFIDDFSKFTWIYLLKYKSEVFEKFKEFQALVERMFDRKIIAMQTDWRGGRYQKLNSFFAQIGLIIMCHVLTLIRQNGSAERKHRHIVEVGLSLLSYASMPLKFWDEAFVAATYLINRIPSKTIQNSTPLEKLFNQK

ProfileScan: PS50994
IPR001584
509-673 INTEGRASE
Integrase, catalytic core

VSQFPLELVFSDVWGPAPESVGRNKYYVSFIDDFSKFTWIYLLKYKSEVFEKFKEFQALVERMFDRKIIAMQTDWRGGRYQKLNSFFAQIGLIIMCHVLTLIRQNGSAERKHRHIVEVGLSLLSYASMPLKFWDEAFVAATYLINRIPSKTIQNSTPLEKLFNQK

Gene3D: G3DSA:3.30.420.10
512-665 G3DSA:3.30.420.10

FPLELVFSDVWGPAPESVGRNKYYVSFIDDFSKFTWIYLLKYKSEVFEKFKEFQALVERMFDRKIIAMQTDWRGGRYQKLNSFFAQIGLIIMCHVLTLIRQNGSAERKHRHIVEVGLSLLSYASMPLKFWDEAFVAATYLINRIPSKTIQNSTP

HMMPfam: PF00665
IPR001584
512-624 rve
Integrase, catalytic core

FPLELVFSDVWGPAPESVGRNKYYVSFIDDFSKFTWIYLLKYKSEVFEKFKEFQALVERMFDRKIIAMQTDWRGGRYQKLNSFFAQIGLIIMCHVLTLIRQNGSAERKHRHIV

HMMPanther: PTHR11439
570-1445 PTHR11439,GAG-POL-RELATED RETROTRANSPOSON

RMFDRKIIAMQTDWRGGRYQKLNSFFAQIGLIIMCHVLTLIRQNGSAERKHRHIVEVGLSLLSYASMPLKFWDEAFVAATYLINRIPSKTIQNSTPLEKLFNQKPDYSSLRVFGCACWPHLRPYNTHKLQFRSKQCVFLGFSTHHKGFKCLDVSSGRVYISRDVVFDENVFPFSTLHSNAGARLRSEILLLPSPLTNYNTASAGGTHVVAPVANTPLPSDNLISNAADVTSGENSAAHEQEMENEQEIENVMHGNDVHGDAASGPVLDQPTADSSTAPDQGADTSDAVSGAASDAGGDTATLGAGAANSAAAGGEESQPVQPDVTGTVLATVAPASRPHTRLRSGIRKEKVYTDGTVKYGCFSSTGEPQNDKEALGDKNWRDAMETEYNALIKNDTWHLVPYEKGQNIIGCKWVYKIKRKADGTLDRYKARLVAKGFKQRYGIDYEDTFSPVVKAATIRIILSIAVSRGWSLRQLDVQNAFLHGFLEEEVYMQQPPGFESSSKPDYVCKLDKALYGLKQAPRAWYSRLSKKLVELGFEASKADTSLFFLNKGGILMFVLVYVDDIIVASSTEKATTALLKDLNKEFALKDLGDLHYFLGIEVTKVSNGVILTQEKYANDLLKRVNMSNCKPVSTPLSVSEKLTLYEGSPLGPNDAIQYRSIVGALQYLTLTRPDIAYSVNKVCQFLHAPTTSHWIAVKRILRYLNQCTSLGLHIHKSASTLVHGYSDADWAGSIDDRKSTGGFAVFLGSNLVSWSARKQPTVSRSSTEAEYKAVANTTAELIWVQTLLKELGIESPKAAKIWCDNLGAKYLSANPVFHARTKHIEVDYHFVRERVSQKLLEIDFVPSGDQVADGFTKALSACLLENFKHNLNLARL

superfamily: SSF56672
962-1400 SSF56672

KNDTWHLVPYEKGQNIIGCKWVYKIKRKADGTLDRYKARLVAKGFKQRYGIDYEDTFSPVVKAATIRIILSIAVSRGWSLRQLDVQNAFLHGFLEEEVYMQQPPGFESSSKPDYVCKLDKALYGLKQAPRAWYSRLSKKLVELGFEASKADTSLFFLNKGGILMFVLVYVDDIIVASSTEKATTALLKDLNKEFALKDLGDLHYFLGIEVTKVSNGVILTQEKYANDLLKRVNMSNCKPVSTPLSVSEKLTLYEGSPLGPNDAIQYRSIVGALQYLTLTRPDIAYSVNKVCQFLHAPTTSHWIAVKRILRYLNQCTSLGLHIHKSASTLVHGYSDADWAGSIDDRKSTGGFAVFLGSNLVSWSARKQPTVSRSSTEAEYKAVANTTAELIWVQTLLKELGIESPKAAKIWCDNLGAKYLSANPVFHARTKHIEVDYHFV

HMMPfam: PF07727
IPR013103
963-1206 RVT_2
Reverse transcriptase, RNA-dependent DNA polymeras

NDTWHLVPYEKGQNIIGCKWVYKIKRKADGTLDRYKARLVAKGFKQRYGIDYEDTFSPVVKAATIRIILSIAVSRGWSLRQLDVQNAFLHGFLEEEVYMQQPPGFESSSKPDYVCKLDKALYGLKQAPRAWYSRLSKKLVELGFEASKADTSLFFLNKGGILMFVLVYVDDIIVASSTEKATTALLKDLNKEFALKDLGDLHYFLGIEVTKVSNGVILTQEKYANDLLKRVNMSNCKPVSTPLS


List of References




List of Contributions

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Analyses

Blast

Blast matches against Reference R-Genes. Show


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