RetrogeneDB ID: | retro_opri_1104 | ||
Retrocopy location | Organism: | Southern American pika (Ochotona princeps) | |
| Coordinates: | scaffold_7133:37211..38673(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STRIP1 | ||
| Ensembl ID: | ENSOPRG00000004063 | ||
| Aliases: | None | ||
| Description: | striatin interacting protein 1 [Source:HGNC Symbol;Acc:25916] |
Retrocopy-Parental alignment summary:
>retro_opri_1104
CGGGGACACCGCAGTTCTCGGAGGCAACTCCTCACTAAGCAAGACAGCCTGGACATCTACAATGAAAGGGATCTCTTCAA
GAATGAAGAGCCAGCCGCGGAGGAGGAAGAGGAGCCTCCCAGGGATGGAGAGCTAGACCTGCTGGAACAGGACCCGCTGG
TCCCTCCTCCACCCTTGCAAGCACCTCTCTCTGCTGATCTGGTGGCTTTTCCCAAGGGCCTTCCTTGGGCCCCCAAAGTC
AGGCAGAAGGACATGGAGCAGTTCTTGGAGATGAGCAGGAACAAGTTCATCGGCTTCACGCTGGGGCAGGACACGGACAC
CTTGGTTGGATTGCCTAGACCCATTCACGAGAGTGTGAAGACCCTTAAGCAGCACAAGTATATCTCCATCGTGGATGTGC
AGATCAAGAATGAGGAGGAGCTGGAGAAGTGTCCCATGTCTCTGGGGGAAGAAGTGGTTCCAGAGACACCATGTGAAATC
CTCTACCAGGGCATGCTGTATAGCCTTCCCCAGTACATGATTGCTCTGCTTAAGATTCTGCTGGCTGCAGCGCCCACCTC
CAAGGCTAAGACAGACTCCATCAACATCCTGGCAGACTTCCTGCCTGAAGAGATGCCCATCTCTGTAGTTCAGAGCATGA
AGCTGGGCATCGATGTGAACAGGCACGAAGAGATCATTGTCAAGAGCATCTCCGCCCTACTCCTGCTCCTTCTCAAACAC
TTCAAACTCAACCACATCTACCAGTTTGAATATGTATCGCAACATTTGGTATTTGCCAGCTGTATCCCTTTGATCCTGAA
GTTCTTCAATCAAAACATCTTGTCCTACATCACTGCCAAGAACAGCATCACCGTCCTGGACTACCCTGGCTGTACCATCT
AGGATTTGCCGCAGCTTACTGCCGAGAGCCTGGAGGCGGGGGACAACAGCCAGCTCTGCTGGAGGAACCTCTTCTCTGCA
TCAACCTCCTGCGGCTGCTCAACAAGCTGACCAAGTGGAAGCATTCCCGGACCATGATGCGCGTGGTGTTTAAATCAGCT
CCAATCTTGAAACGAGCCCTCAAGGTCAAACAGGCCATGCTGCAACTTTATGTCCTGAAGCTGCTGAAGATACAGATCAA
GTACCTGGGGCGCCAGTGGAGAAAGAGCAACATGAAAACCATGCCAGCCATTTACCAGAAAGTGCGCCACCGCATGAACG
ACGACTGGGCTTACGGGAACGACATCGATGCCAGGCCGTGGGACTTCCAGGCAGAGGAATGCACGCTGAGGGCCAACATT
GAGGCTTTCAACAGCCGCCGCTACGACAGAACCCGGGACTCGGAGTTCTCAACTGTGGATAACTGCTTGCAGAGCATGCT
GGACAGAGGCTGGATCTGCCTGAAGATTTCCACTATTCGTATGAGCTCTGGCTGGAGAGAGAGGTGTTTTCCCAGCCCAT
CTGCTGGGAGGAGCTGCTCCAG
ORF - retro_opri_1104 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.7 % |
| Parental protein coverage: | 58.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RGRREHKA--LIKQDNLDAFNERDPYKADDSREEEEENDDDNSLEGETFPLERDEVMPPP-LQHP-QTDR |
| RG.R......L.KQD.LD..NERD..K......EEEE........GE...LE.D...PPP.LQ.P...D. | |
| Retrocopy | RGHRSSRRQLLTKQDSLDIYNERDLFKNEEPAAEEEE---EPPRDGELDLLEQDPLVPPPPLQAPLSADL |
| Parental | LTCPKGLPWAPKVREKDIEMFLESSRSKFIGYTLGSDTSTIVGLPRPIHESIKTLKQHKYTSIAEVQAQM |
| ...PKGLPWAPKVR.KD.E.FLE.SR.KFIG.TLG.DT.T.VGLPRPIHES.KTLKQHKY.SI..VQ... | |
| Retrocopy | VAFPKGLPWAPKVRQKDMEQFLEMSRNKFIGFTLGQDTDTLVGLPRPIHESVKTLKQHKYISIVDVQIKN |
| Parental | EEEYLRSPLSGGEEEVEQVPAETLYQGLLPSLPQYMIALLKILLAAAPTSKAKTDSINILADVLPEEMPT |
| EEE....P.S.GEE.V...P.E.LYQG.L.SLPQYMIALLKILLAAAPTSKAKTDSINILAD.LPEEMP. | |
| Retrocopy | EEELEKCPMSLGEEVVPETPCEILYQGMLYSLPQYMIALLKILLAAAPTSKAKTDSINILADFLPEEMPI |
| Parental | TVLQSMKLGVDVNRHKEVIVKAISAVLLLLLKHFKLNHVYQFEYMAQHLVFANCIPLILKFFNQNIMSYI |
| .V.QSMKLG.DVNRH.E.IVK.ISA.LLLLLKHFKLNH.YQFEY..QHLVFA.CIPLILKFFNQNI.SYI | |
| Retrocopy | SVVQSMKLGIDVNRHEEIIVKSISALLLLLLKHFKLNHIYQFEYVSQHLVFASCIPLILKFFNQNILSYI |
| Parental | TAKNSISVLDYPHCVVHELPELTAESLEAGDNNQFCWRNLFS-CINLLRILNKLTKWKHSRTMMLVVFKS |
| TAKNSI.VLDYP.C....LP.LTAESLEAGDN.Q.CWRNLFS.CINLLR.LNKLTKWKHSRTMM.VVFKS | |
| Retrocopy | TAKNSITVLDYPGCTI*DLPQLTAESLEAGDNSQLCWRNLFS<CINLLRLLNKLTKWKHSRTMMRVVFKS |
| Parental | APILKRALKVKQAMMQLYVLKLLKVQTKYLGRQWRKSNMKTMSAIYQKVRHRLNDDWAYGNDLDARPWDF |
| APILKRALKVKQAM.QLYVLKLLK.Q.KYLGRQWRKSNMKTM.AIYQKVRHR.NDDWAYGND.DARPWDF | |
| Retrocopy | APILKRALKVKQAMLQLYVLKLLKIQIKYLGRQWRKSNMKTMPAIYQKVRHRMNDDWAYGNDIDARPWDF |
| Parental | QAEECALRANIERFNARRYDRAHSNPDFLPVDNCLQSVL-GQRVDLPEDFQMNYDLWLEREVFSKPISWE |
| QAEEC.LRANIE.FN.RRYDR......F..VDNCLQS.L.GQR.DLPEDF...Y.LWLEREVFS.PI.WE | |
| Retrocopy | QAEECTLRANIEAFNSRRYDRTRDS-EFSTVDNCLQSML<GQRLDLPEDFHYSYELWLEREVFSQPICWE |
| Parental | ELLQ |
| ELLQ | |
| Retrocopy | ELLQ |
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_1104 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ochotona princeps | ENSOPRG00000004063 | 1 retrocopy |
retro_opri_1104 ,
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