RetrogeneDB ID: | retro_opri_978 | ||
Retrocopy location | Organism: | Southern American pika (Ochotona princeps) | |
| Coordinates: | scaffold_5212:119628..121128(-) | ||
| 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_978
TGCCCGACAACCGAGGTCACCAATACATTTATTCGTCTGTGTGAGCGATTTCACGACAGAACGCCACCCGAACTGATCGG
TGTTCATTGTACCCATGGTTTCAATCGTACTGGCTTCCTCATTTGTGCCTTTTTGGTGGAGAACATGGATTGGAGCATTG
AAGCAGCAGTTGCTACTTTTGCCCAAGCCAGACCACCAGGAATCTATAAGGGCGATTATTTGAAGGAACTCTTTTGGCGC
TATGGCGCTAGAGAAGCACCACCCCCACCTCTCTTGCCAGATTGGTGTTTGGAGGATGAGCAAGATGAAGGTGAGGAAGA
GGATGGAAACAAGGAATCAGAACCCAGATCAAGTGCTTCCTTTGGCAAAAGGAGGAAAGAAAGGTTGAAAGTGGGTGCCA
TTTTCTTGGAAGGTATAACTGTGAACGGTGTGACTCAAGTAACAACTCAACCAAAGCTAGGAGAGGTACAACAGAAGTGT
CATCAATTCTGTGGCTGGGAAGGGTCTGGATTCCCTGGAGCACAGCCCGTTTCCATGGACAAGCAAAATATTACACTTTT
AGAGCAGAAGCCATATAAAGTAAGCTGGAAAGCAGATGGCACTCGTTACATGATGTTGGTTGATGGCACAAATGAAGTCT
TTATGATTGATCGAGATAATTCAGTGTTTCATGTTTCTAATCTGGAATTTCCATGTCGGAAAGACCTTCAAATCCATTTA
TCGAATACTCTTTTGGATGGCGAGATGATTATTGACAGAGTAAACGGACAGGCTCTTCCTAGATATTTGATATATGACAT
CATTAAATTCAATGCACAGCCAGTTGGAGATTGCGACTTGAATGTCCGCTTGCAGTGTATAGAACGAGAAATTATAAATC
CTCGGCACGAGAAAATGAAGACCGGACTCATTGACAAGACACGGGAACCATTTAGTGTCAGAAAGAAGCCGTTTTTTGAC
ATTCATACTTCAAGAAAGCTGCTTGAAGGAAATTTTGCCAAACAAGTCAGTCATGCAGTGGATGGACTTATATTTCAGCC
CATCGGGAAGTATAAGCCTGGTCGGTGTGATGATATTTTGAAGTGGAAACCTCCCAGTTTGAATTCTGTGGATTTCCGCC
TGAAGATAACAAGACTGGGAGGAGAAGGGCTACTTCCTCAGAATGCCGGTCTTCTCTATGTTGGAGGCTACGAAAGACCC
TTTGCCCAAATCAAGGTGACAAAAGAGCTCAATCAGTATGACAACAAAATCATAGAATGCAGATTTGAGAAGAACAGCTG
GGTCTTCATGAGACCGAGAACAGACAAAAGTTTTCCGAATGCCTATAACACTGCCATGGCTGTGTGCAATAGCATCTCAA
ACCCTGTCACCAAGGAGATGCTGTTTGAGTTCATCGACGGATGTGCTGCAGCTTTTCAAGGACAGAAGCAAAAGCATCAT
CTGAGCCCCGACACAGAGCTCATGCCCCTGCCGCCTCCCAAAAGACCGCGCCCTGCCACC
ORF - retro_opri_978 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.42 % |
| Parental protein coverage: | 87.13 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CPTTEVTNTFIRLCERFNDRTPPELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYK |
| CPTTEVTNTFIRLCERF.DRTPPELIGVHCTHGFNRTGFLICAFLVE.MDWSIEAAVATFAQARPPGIYK | |
| Retrocopy | CPTTEVTNTFIRLCERFHDRTPPELIGVHCTHGFNRTGFLICAFLVENMDWSIEAAVATFAQARPPGIYK |
| Parental | GDYLKELFRRYGDIEEAPPPPLLPDWCFEDDEDEDEEEDGKKESEPGSSASFGKRRKERLKLGAIFLEGI |
| GDYLKELF.RYG...EAPPPPLLPDWC.ED..DE.EEEDG.KESEP.SSASFGKRRKERLK.GAIFLEGI | |
| Retrocopy | GDYLKELFWRYG-AREAPPPPLLPDWCLEDEQDEGEEEDGNKESEPRSSASFGKRRKERLKVGAIFLEGI |
| Parental | TVKGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIKLLEQKPYKVSWKADGTRYMMLIDG |
| TV.GVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNI.LLEQKPYKVSWKADGTRYMML.DG | |
| Retrocopy | TVNGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNITLLEQKPYKVSWKADGTRYMMLVDG |
| Parental | TNEVFMIDRDNSVFHVSNLEFPFRKDLRIHLSNTLLDGEMIIDRVNGQAVPRYLIYDIIKFNAQPVGDCD |
| TNEVFMIDRDNSVFHVSNLEFP.RKDL.IHLSNTLLDGEMIIDRVNGQA.PRYLIYDIIKFNAQPVGDCD | |
| Retrocopy | TNEVFMIDRDNSVFHVSNLEFPCRKDLQIHLSNTLLDGEMIIDRVNGQALPRYLIYDIIKFNAQPVGDCD |
| Parental | FNIRLQCIEREIINPRHEKMKTGLIDKTQEPFGVRNKPFFDIHTSRKLLEGNFAKAVSHEMDGLIFQPIG |
| .N.RLQCIEREIINPRHEKMKTGLIDKT.EPF.VR.KPFFDIHTSRKLLEGNFAK.VSH..DGLIFQPIG | |
| Retrocopy | LNVRLQCIEREIINPRHEKMKTGLIDKTREPFSVRKKPFFDIHTSRKLLEGNFAKQVSHAVDGLIFQPIG |
| Parental | KYKPGRCDDILKWKPPSLNSVDFRLKITRMGGEGLLPQNVGLLYVGGYERPFAQIKVTKELKQYDNKIIE |
| KYKPGRCDDILKWKPPSLNSVDFRLKITR.GGEGLLPQN.GLLYVGGYERPFAQIKVTKEL.QYDNKIIE | |
| Retrocopy | KYKPGRCDDILKWKPPSLNSVDFRLKITRLGGEGLLPQNAGLLYVGGYERPFAQIKVTKELNQYDNKIIE |
| Parental | CKFENNSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAAAFQGQKRKHHLDPDAELMP |
| C.FE.NSWVFMR.RTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFID.CAAAFQGQK.KHHL.PD.ELMP | |
| Retrocopy | CRFEKNSWVFMRPRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDGCAAAFQGQKQKHHLSPDTELMP |
| Parental | PPPPKRPRPAT |
| .PPPKRPRPAT | |
| Retrocopy | LPPPKRPRPAT |
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_978 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,
|