RetrogeneDB ID: | retro_tsyr_1839 | ||
Retrocopy location | Organism: | Tarsier (Tarsius syrichta) | |
| Coordinates: | scaffold_61689:3937..5675(-) | ||
| 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_1839
AATCCTTTAACGTTGGAGTCCGTGAAGCGACTGGTAGCAGAAGGCAATGAAGAAGAGCTGCACAGATGTTTTGGGGCCCG
GATGGAGGTCGAGACAGCTGGCCTGCGAGCTGCCATGGGAGTAGGAACCTCCTGCATGAACGACTTGACCATCATCCAGA
CTACGCAGGGATTTTGCAGATACCTGGAAAAACAATTCAGTGACCCGAAGCAGAGAGGTGTCGTGATCAACTTTGACGCA
CGGGCCCATCCTCCCAGTGGCGGCAGCAGCTGAAGGTTTGCCCGACTTGCTGCGACCATGTTCATCAGTCAGGGGATTCC
TGTATACCTCTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTACACAGTATCACATCTGAAACTCTGTGCGGGGATCAT
GGACACCGCTTCCCACAACCCGAAGCAAGATAATAGCTACAAGGTCTACTGGGATAAGGGAGCTCAGATCATCTCTCCTC
ATGACAAAGGGATTTCTCAAGCTATTGAAGAAAATCTAGAGCCATGGCCTCAAGCTTGGAACGACTCTTCAATTGATGAC
AGCCCACTGCTGCACGACCCAAATGCTTCCATCAATAACGACTACTTTGAAGACCTTAAAAAATACTGTTTCCACAGGAA
TGTGAACAGAGAGACCAAGGTGAAGTTCGTGCACACCTTCGTCCACGGGGTGGGGCATAACTTCGTGCAGTCGGCTTTCA
AGGCTTTTGACCTTGTTCCTCCTGAGGCCGTGTCCAAGCAGAAAGATCCTGATCCTGAGTTCCCGAGAGTGAAATACCCA
TATCCAGAAGAGGGTAAAGGTGTCTTGACTTCGTCTTTTGCTTTCACTGACAAAACCAAAACTAAAATTGTGCTAGCAAA
TGACCCAGATGCGGATAGACTTGCTGTGGCAGAAAAGCAAGACAGTGGTGAATGGAGAGTGTTTTCAGGCATGAGTTGGG
GGCGCTCCTGTGTTGGTGGCTTTTTACTTCTTGGAAAGAAAAGAACAAGGACCGCAGTGCCCTCAAAGACACCTACATGT
TGTCTAGCACCGTCTCCTCCAAAATCCTGCGTGCCATCGCCTTAACGGAGGGTTTCCATATCGAGGAAACATTAACTGGT
TTTAAGTGGATGGGTAACAGAGCCAAGCAGCTGCTAGACCAGGGAAAAACTGTCTTGTTTGCATTTGAGGAAGCTATTGG
ATATATGTGCTGCCCTTTTGTCCAGGACAAAGATGGAGTCAGTGCCGCTGTCATAGGCGCAGAGCTGGCCAGTTTTCTAG
CTACCAAGAACCTTTTATGTCTCACCAGCTGAAGGCCATCTACATGGAGTATGGCTATCATCTTACCAAAGCTTTCTGTT
TTATCTGATATGATCAAACCATTATTGAAACATTATTTGAAAACCTCCGAAACTACGATGGGAAAAAATCACTATCCAAA
AATGTGTGGCAGATTTGAAATATCTGCCATTAGGGACCTCACCACTGGCTATGGCGACAGCCAACCTGATAAAAAGGCTG
TTCTTCCCACGAGTAAAAGCAGCCAAATGATAACATTCACCTTTGCCAATGGAGGAGTGGCCACCATGCGAACCAGTGGG
ACTGAGCCCAAAATCAAGTACTACACAGAACTGTGTGCCCCTCCTGGAAACAGTGACCCTGAGCAGCTGAAGAAGGAACT
GAATGAACTAGTCAGTGCGATTGAAGAACATTTTTTCCAGGCACAAAAGTACAATTTG
ORF - retro_tsyr_1839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.58 % |
| Parental protein coverage: | 99.15 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
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 | QRGVVINFDARAHPPSGGSS*RFARLAATMFISQGIPVYLFSGITPTP<FVPYTVSHLKLCAGIMDTASH |
| Parental | NRKEDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKI |
| N.K.DN.YKVYW..GAQI.SPHDK.I...IEE..EPW...WND...D.SPL..DP...I...Y.EDLKK. | |
| Retrocopy | NPKQDNSYKVYWDKGAQIISPHDKGISQAIEENLEPWPQAWNDSSIDDSPLLHDPNASINNDYFEDLKKY |
| Parental | CFYRELNSKTTLKFVHTSFHGVGHDYVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELS |
| CF.R..N..T..KFVHT..HGVGH..VQ.AF..F...PP..V..QKDPDPEF..VK.P.PEEG..VL..S | |
| Retrocopy | CFHRNVNRETKVKFVHTFVHGVGHNFVQSAFKAFDLVPPEAVSKQKDPDPEFPRVKYPYPEEGKGVLTSS |
| Parental | LRLAEKENARIVLATDPDADRLAVAELQENGHWKVFTG-NELAALFGWWMFDCWR-KNKPRNADVKNIYM |
| .....K....IVLA.DPDADRLAVAE.Q..G.W.VF.G..EL.AL..WW.F..W..KNK.R.A..K..YM | |
| Retrocopy | FAFTDKTKTKIVLANDPDADRLAVAEKQDSGEWRVFSG<HELGALLCWWLFTSWKEKNKDRSA-LKDTYM |
| Parental | LATTVSSKILKAIAFKEGFHFEETLPGFKWIGSRIKDLLENGKEVLFAFEESIGFLCGTSVLDKDGVSAA |
| L..TVSSKIL.AIA..EGFH.EETL.GFKW.G.R.K.LL..GK.VLFAFEE.IG..C...V.DKDGVSAA | |
| Retrocopy | LSSTVSSKILRAIALTEGFHIEETLTGFKWMGNRAKQLLDQGKTVLFAFEEAIGYMCCPFVQDKDGVSAA |
| Parental | VVVAEMASYLETMNVT-LKQQLIKVYEKYGYHISKTSYFLCYDPLTIKSIFERLRNFDSPK-EYPKFCGT |
| V..AE.AS.L.T.N......QL...Y..YGYH..K...F..YD...I...FE.LRN.D..K..YPK.CG. | |
| Retrocopy | VIGAELASFLATKNLL<MSHQLKAIYMEYGYHLTKAFCFI*YDQTIIETLFENLRNYDGKK>HYPKMCGR |
| Parental | FAILHVRDITTGYDSSQPNKKSVLPVSKNSQMITFTFQNGCVATLRTSGTEPKIKYYAEMCASPDQSDTA |
| F.I...RD.TTGY..SQP.KK.VLP.SK.SQMITFTF.NG.VAT.RTSGTEPKIKYY.E.CA.P..SD.. | |
| Retrocopy | FEISAIRDLTTGYGDSQPDKKAVLPTSKSSQMITFTFANGGVATMRTSGTEPKIKYYTELCAPPGNSDPE |
| Parental | LLEEELKKLIEALIENFLQPSKNGL |
| .L..EL..L..A..E.F.Q..K..L | |
| Retrocopy | QLKKELNELVSAIEEHFFQAQKYNL |
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_1839 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,
|