RetrogeneDB ID: | retro_opri_979 | ||
Retrocopy location | Organism: | Southern American pika (Ochotona princeps) | |
| Coordinates: | scaffold_5212:123577..125299(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNGTT | ||
| Ensembl ID: | ENSOPRG00000000916 | ||
| Aliases: | None | ||
| Description: | RNA guanylyltransferase and 5'-phosphatase [Source:HGNC Symbol;Acc:10073] |
Retrocopy-Parental alignment summary:
>retro_opri_979
AGATTCTTGCCTCTCAAGACAATGTTAGGACCAAGATACGATAGTCAAGTTGCTGAAGAAAATCGATTCCATCCCACCAT
GCTCTCCAATTATCTCAAGAGTCGAAAGGTGAAAATGAGCTTATTGGTAGACTTGACCAACACTTCAAGATTCTATGATA
GGAGTGACATAGAAAAAGAAGGAATTACGTATGTAAAGCTTCCGTGTAAAGGACATGGTGAGTGCCCGACAACCGAGGTC
ACCAATACATTTATTCGTCTGTGTGAGCAGTTTCACGACAGAACGCCACCCGAACTGATCGGTGTTCATTGTACCCATGG
TTTCAATCGTACTGGCTTCCTCATTTGTGCCTTTTTGGTGGAGAACATGGATTGGAGCATTGAAGCAGCAGTTGCTACTT
TTGCCCAAGCCAGACCACCAGGAATCTATAAGGGCGATTATTTGAAGGAACTCTTTTGGCGCTATGGCGCTAGAGAAGCA
CCAACCCCACCTCTCTTGCCAGCTTGGTGTTTGGAAGATGAGGAAGATGAAGGGGAGGAAGAGGATGGGAACAAGAAATC
AGAGCCCGGATCAAGTGCTTCCTTTGGCAAAAGGAGGAAAGAAAGGTTGAAAGTGGGTGCCATTTTCTTGGAAGGTATAA
CTGTGAACGGTGTGACTCAAGTAACAACTCAACCAAAGCTAGGAGAGGTACAACAGAAGTGTCATCAATTTTGTGGCTGG
GAAGGGTCTGGATTCCCTGGAGCACAGCCCGTTTCCATGGACAAGCAAAATATTACACTTTTAGAGCAGAAGCCATATAA
AGTAAGCTGGAAAGCAGATGGCACTCGTTACATGATGTTGGTTGATGGCACAAATGAAGTCTTTATGATTGATCGAGATA
ATTCAGTGTTTCATGTTTCTAATCTGGAATTTCCATGTCGGAAAGACCTTCAAATCCATTTATCGAATACTCTTTTGGAT
GGCGAGATGATTATTGACAGAGTAAACGGACAGGCTCTTCCTAGATATTTGATATATGACATCATTAAATTCAATGCACA
GCCAGTTGGAGATTGCGACTTGAATGTCCGCTTGCAGTGTATAGAACGAGAAATTATAAATCCTCGGCACGAGAAAATGA
AGACCGGACTCATTGACAAGACACGGGAACCATTTAGTGTCAGAAAGAAGCCGTTTTTTGACATTCATACTTCAAGAAAG
CTGCTTGAAGGAAATTTTGCCAAACAAGTCAGTCATGCAGTGGATGGACTTATATTTCAGCCCATCGGGAAGTATAAGCC
TGGTCGGTGTGATGATATTTTGAAGTGGAAACCTCCCAGTTTGAATTCTGTGGATTTCCGCCTGAAGATAACAAGACTGG
GAGGAGAAGGGCTACTTCCTCAGAATGCCGGTCTTCTCTATGTTGGAGGCTACAAAAGACCCTTTGCCCAAATCAAGGTG
ACAAAAGAGCTCAATCAGTATGACAACAAAATCATAGAATGCAGATTTGAGAAGAACAGCTGGGTCTTCATGAGACAGAG
AACAGACAAAAGTTTTCCGAATGCCTATAACACTGCCATGGCTGTGTGCAATAGCATCTCAAACCCTGTCACCAAGGAGA
TGCTGTTTGAGTTCATCGACAGATGTGCTGCAGCTTTTCAAGGACAGAAGCAAAAGCATCATCTGAACCCTGACACACAG
CTCATGCCCCCGCCGCCTCCCAAAAGACCACGCCCTGCCACC
ORF - retro_opri_979 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.13 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RFLPLKTMLGPRYDSQVAEENRFHPSMLSNYLKSLKXXXXXXVDLTNTSRSYDRNDIEKEGITYIKLQCK |
| RFLPLKTMLGPRYDSQVAEENRFHP.MLSNYLKS.K......VDLTNTSR.YDR.DIEKEGITY.KL.CK | |
| Retrocopy | RFLPLKTMLGPRYDSQVAEENRFHPTMLSNYLKSRKVKMSLLVDLTNTSRFYDRSDIEKEGITYVKLPCK |
| Parental | GHGECPTTEVTNTFIRLCERFNDRTPPELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPP |
| GHGECPTTEVTNTFIRLCE.F.DRTPPELIGVHCTHGFNRTGFLICAFLVE.MDWSIEAAVATFAQARPP | |
| Retrocopy | GHGECPTTEVTNTFIRLCEQFHDRTPPELIGVHCTHGFNRTGFLICAFLVENMDWSIEAAVATFAQARPP |
| Parental | GIYKGDYLKELFRRYGDIEEAPPPPLLPDWCFEDDEDEDEEEDGKKESEPGSSASFGKRRKERLKLGAIF |
| GIYKGDYLKELF.RYG...EAP.PPLLP.WC.ED.EDE.EEEDG.K.SEPGSSASFGKRRKERLK.GAIF | |
| Retrocopy | GIYKGDYLKELFWRYG-AREAPTPPLLPAWCLEDEEDEGEEEDGNKKSEPGSSASFGKRRKERLKVGAIF |
| Parental | LEGITVKGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIKLLEQKPYKVSWKADGTRYMM |
| LEGITV.GVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNI.LLEQKPYKVSWKADGTRYMM | |
| Retrocopy | LEGITVNGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNITLLEQKPYKVSWKADGTRYMM |
| Parental | LIDGTNEVFMIDRDNSVFHVSNLEFPFRKDLRIHLSNTLLDGEMIIDRVNGQAVPRYLIYDIIKFNAQPV |
| L.DGTNEVFMIDRDNSVFHVSNLEFP.RKDL.IHLSNTLLDGEMIIDRVNGQA.PRYLIYDIIKFNAQPV | |
| Retrocopy | LVDGTNEVFMIDRDNSVFHVSNLEFPCRKDLQIHLSNTLLDGEMIIDRVNGQALPRYLIYDIIKFNAQPV |
| Parental | GDCDFNIRLQCIEREIINPRHEKMKTGLIDKTQEPFGVRNKPFFDIHTSRKLLEGNFAKAVSHEMDGLIF |
| GDCD.N.RLQCIEREIINPRHEKMKTGLIDKT.EPF.VR.KPFFDIHTSRKLLEGNFAK.VSH..DGLIF | |
| Retrocopy | GDCDLNVRLQCIEREIINPRHEKMKTGLIDKTREPFSVRKKPFFDIHTSRKLLEGNFAKQVSHAVDGLIF |
| Parental | QPIGKYKPGRCDDILKWKPPSLNSVDFRLKITRMGGEGLLPQNVGLLYVGGYERPFAQIKVTKELKQYDN |
| QPIGKYKPGRCDDILKWKPPSLNSVDFRLKITR.GGEGLLPQN.GLLYVGGY.RPFAQIKVTKEL.QYDN | |
| Retrocopy | QPIGKYKPGRCDDILKWKPPSLNSVDFRLKITRLGGEGLLPQNAGLLYVGGYKRPFAQIKVTKELNQYDN |
| Parental | KIIECKFENNSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAAAFQGQKRKHHLDPDA |
| KIIEC.FE.NSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAAAFQGQK.KHHL.PD. | |
| Retrocopy | KIIECRFEKNSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAAAFQGQKQKHHLNPDT |
| Parental | ELMPPPPPKRPRPAT |
| .LMPPPPPKRPRPAT | |
| Retrocopy | QLMPPPPPKRPRPAT |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_979 was not experimentally validated.
Retrocopy orthology:
Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000003302 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000000916 | 3 retrocopies |
retro_opri_523, retro_opri_978, retro_opri_979 ,
|