RetrogeneDB ID: | retro_tsyr_721 | ||
Retrocopy location | Organism: | Tarsier (Tarsius syrichta) | |
| Coordinates: | scaffold_18142:22668..24407(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PGM2L1 | ||
| Ensembl ID: | ENSTSYG00000002928 | ||
| Aliases: | None | ||
| Description: | phosphoglucomutase 2-like 1 [Source:HGNC Symbol;Acc:20898] |
Retrocopy-Parental alignment summary:
>retro_tsyr_721
AATCCTTTAACGTTGGAGTCCGTGAAGCGACTGGTAGCAGAAGGCAATGAAGAAGAGCTGCACAGATGTTTTGGGGCCCG
GATGGAGGTCGAGACAGCTGGCCTGCGAGCTGCCATGGGAGTAGGAACCTCCTGCATGAACGACTTGACCATCATCCAGA
CTACGCAGGGATTTTGCAGATACCTGGAAAAACAATTCAGTGACCCGAAGCAGAGAGGTGTCGTGATCAGCTTTGACGCA
CGGGCCCATCCTCCCAGTGGCGGCAGCAGCCGCAGGTTTGCCCGACTTGCTGCGACCATGTTCATCAGTCAGGGGATTCC
TGTATACCTCTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTACACAGTATCACATCTGAAACTCTGTGCGGGGATCAT
GGTCACCGCTTCCCACAACCCGAAGCAGGATAATAGCTACGAGGTCTACTGGGATAAGGAAGCTCAGATCATCTCTCCTC
ATGACAAAGGGATTTCTCAAGCTATTGAAGAAAATCTAGAGCCATGGCCTCAAGCTTGGGACGACTCTTCAATTGATGGC
AGCCCACTGCTGCACGACCCAAATGCTTCCATCAATAACGACTACTTTGAAGACCTTAAAAAATACTGTTTCCACAGGAA
TGTGAACAGAGAGACCAAGGTGAAGTTCGTGCACACCTTCGTCCACGGGGTGGGGCATAACTTCGTGCAGTCGGCTTTCA
AGGCTTTTGACCTTGTTCCTCCTGAGGCCGTGTCCAAGCAGAAAGATCCTGATCCTGAGTTCCCGAGAGTGAAATACCCA
AATCCCGAAGAGGGTAAAGGTGTCTTGACTTTGTCTTTTGCTTTGGCTGACAAAACCAAAACTAAAATTGTGCTAGCAAA
TGACCCAGATGCGGATAGACTTGCTGTGGCAGAAAAACAAGTCAGTGGTGAATGGAGAGTGTTTTCAGGCAATGAGTTGG
GGGCGCTCCTGGGCTGGTGGTTTTATACTTCTTGGAAAGAAAAGAACAAGGACCGCAGTGCCCTCAAAGACACCTACATG
TTGTCTAGCACCGTCTCCTCCAAAATCCTGCGTGCCATCGCCTTAAAGGAGGGTTTCCATATCGAGGAAAAGTTCACTGG
CTTTAAGTGGATGGGTAACAGAGCCAAGTAGCTGCTAGACCAGGTAAAAACTGTCTTGTTTGCATTTGAGGAAGCTATGG
GATATATGTGCTGCCCTTTTGTCCAGGACAAAGATGGAGTCAGTGCCGCTGTCATAGGCGCAGAGCTGGCCAGTTTTCTA
GCTACCAAGAATCTTTCTATGTCTCAGCAGCTGAAGGCCATCTACATGGAGTATGGCTATCACCTTACCAAAGCTTTCTG
TTTTATCTGACATGATCAAACCATCATTGAAACATTATTTGAAAACCTCCGAAACTACGATGGGAAAAACCACTATCCAA
AAATGTGTGGCAGATTTGAAATATCTGCCATTAGGGACCTCACCACTGGCTATGGCGACAGCCAACCTGATAAAAAGGCT
GTTCTTCCCACGAGTAAAAGCAGCCAAATGACAACATTCACCTTTGCCAGTGGAGGAATAGCCACCATGTGGACCAGTGG
GATGGAGCCCCAAATCAAGCTCTACACAGAACTGTGTGCCCCTCATGGAAACAGTGATCCTGAGTAGCTGAAGAAGGAAC
TGAGTGAACTAGTCAGTGCGATTGAAGAACATTTTTTCCAGCCAAAAAAGGACAATTTG
ORF - retro_tsyr_721 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.33 % |
| Parental protein coverage: | 99.15 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NPKTKEQIENLLRNGMNKELRDRLCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFK |
| NP.T.E....L...G...EL......RM...TAGLR.AMG.G....NDLT.IQ.TQG...YLE..FSD.K | |
| Retrocopy | NPLTLESVKRLVAEGNEEELHRCFGARMEVETAGLRAAMGVGTSCMNDLTIIQTTQGFCRYLEKQFSDPK |
| Parental | QRGFVVGYDTRGQVTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTP-FVPYAVQELKAVAGVMITASH |
| QRG.V...D.R....S..SS.R.A.L.A........PVYLFS...PTP.FVPY.V..LK..AG.M.TASH | |
| Retrocopy | QRGVVISFDARAHPPSGGSSRRFARLAATMFISQGIPVYLFSGITPTP<FVPYTVSHLKLCAGIMVTASH |
| Parental | NRKEDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKI |
| N.K.DN.Y.VYW...AQI.SPHDK.I...IEE..EPW...W.D...D.SPL..DP...I...Y.EDLKK. | |
| Retrocopy | NPKQDNSYEVYWDKEAQIISPHDKGISQAIEENLEPWPQAWDDSSIDGSPLLHDPNASINNDYFEDLKKY |
| Parental | CFYRELNSKTTLKFVHTSFHGVGHDYVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELS |
| CF.R..N..T..KFVHT..HGVGH..VQ.AF..F...PP..V..QKDPDPEF..VK.PNPEEG..VL.LS | |
| Retrocopy | CFHRNVNRETKVKFVHTFVHGVGHNFVQSAFKAFDLVPPEAVSKQKDPDPEFPRVKYPNPEEGKGVLTLS |
| Parental | LRLAEKENARIVLATDPDADRLAVAELQENGHWKVFTGNELAALFGWWMFDCWR-KNKPRNADVKNIYML |
| ..LA.K....IVLA.DPDADRLAVAE.Q..G.W.VF.GNEL.AL.GWW....W..KNK.R.A..K..YML | |
| Retrocopy | FALADKTKTKIVLANDPDADRLAVAEKQVSGEWRVFSGNELGALLGWWFYTSWKEKNKDRSA-LKDTYML |
| Parental | ATTVSSKILKAIAFKEGFHFEETLPGFKWIGSRIKDLLENGKEVLFAFEESIGFLCGTSVLDKDGVSAAV |
| ..TVSSKIL.AIA.KEGFH.EE...GFKW.G.R.K.LL...K.VLFAFEE..G..C...V.DKDGVSAAV | |
| Retrocopy | SSTVSSKILRAIALKEGFHIEEKFTGFKWMGNRAK*LLDQVKTVLFAFEEAMGYMCCPFVQDKDGVSAAV |
| Parental | VVAEMASYLETMNVTLKQQLIKVYEKYGYHISKTSYFLCYDPLTIKSIFERLRNFDSPKEYPKFCGTFAI |
| ..AE.AS.L.T.N....QQL...Y..YGYH..K...F...D...I...FE.LRN.D....YPK.CG.F.I | |
| Retrocopy | IGAELASFLATKNLSMSQQLKAIYMEYGYHLTKAFCFI*HDQTIIETLFENLRNYDGKNHYPKMCGRFEI |
| Parental | LHVRDITTGYDSSQPNKKSVLPVSKNSQMITFTFQNGCVATLRTSGTEPKIKYYAEMCASPDQSDTALLE |
| ...RD.TTGY..SQP.KK.VLP.SK.SQM.TFTF..G..AT..TSG.EP.IK.Y.E.CA....SD...L. | |
| Retrocopy | SAIRDLTTGYGDSQPDKKAVLPTSKSSQMTTFTFASGGIATMWTSGMEPQIKLYTELCAPHGNSDPE*LK |
| Parental | EELKKLIEALIENFLQPSKNGL |
| .EL..L..A..E.F.QP.K..L | |
| Retrocopy | KELSELVSAIEEHFFQPKKDNL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Tarsius syrichta was not studied using RNA-Seq expression data.
Tarsius syrichta was not studied using ChIP-Seq data.
Tarsius syrichta was not studied using EST data.
Tarsius syrichta was not studied using FANTOM5 data.
retro_tsyr_721 was not experimentally validated.
Retrocopy orthology:
Tarsius syrichta 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 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000009209 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000002928 | 7 retrocopies |
retro_tsyr_1740, retro_tsyr_1839, retro_tsyr_2095, retro_tsyr_2112, retro_tsyr_2119, retro_tsyr_721 , retro_tsyr_849,
|