RetrogeneDB ID: | retro_tsyr_2119 | ||
Retrocopy location | Organism: | Tarsier (Tarsius syrichta) | |
| Coordinates: | scaffold_92844:1..1455(+) | ||
| 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_2119
CTTGCTGCGACCATGTTCATCAGTCAGGGGATTCCTGTATACCTCTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTAC
ACAGTATCACATCTGAAACTCTGTGCGGGGATCATGGACACCGCTTCCCACAACCCGAAGCAAGATAATAGCTACAAGGT
CTACTGGGATAAGGGAGCTCAGATCATCTCTCCTCATGACAAAGGGATTTCTCAAGCTATTGAAGAAAATCTAGAGCCAT
GGCCTCAAGCTTGGGACGACTCTTCAATTGATGACAGCCCACTGCTGCACGACCCAAATGCTTCCATCAATAACGACTAC
TTTGAAGACCTTAAAAAATACTGTTTCCACAGGAGTGTGAACAGAGAGACCAAGGTGAAGTTCGTGCACACCTTCGTCCA
CGGGGTGGGGCATAACTTCGTGCAGTCGGCTTTCAAGGCTTTTGACCTTGTTCCTCCTGAGGCCGTGTCCAAGCAGAAAG
ATCCTGATCCTGAGTTCCCGAGAGTGAAATACCCAAATCCCGAAGAGGGTAAAGGTGTCTTGACTTCGTCTTTTGCTTTC
GCTGACAAAACCAAAACTAAAATTGTGCTAGCAAATGACCCAGATGCGGATAGACTTGCTGTGGCAGAAAAGCAAGACAG
TGGTGAATGGAGAGTGTTTTCAGGCAATGAGTTGGGGGCGCTCCTGGGCTGGTGGCTTTTTACTTCTTGGAAAGAAAAGA
ACAAGGACCGCAGTGCCCTCAAAGACACCTACATGTTGTCTAGCACCGTCTCCTCCAAAATCCTGCGTGCCATCGCCTTA
ACGGAGGGTTTCCATATCGAGGAAACATTAACTGGCTTTAAGTGGATGGGTATCAGAGCCAAGCAGCTGCTAGACCAGGG
AAAAACTGTCTTGTTTGCATTTGAGGAAGCTATGGGATATATGTGCTGCCCTTTTGTCCTGGACAAAGATGGAGTCAGTG
CCGCTGTCATAGGCGCAGAGCTGGCCAGTTTTCTAGCTACCAAGAATCTTTCTATGTCTCAGCAGCGTAAGGCCATCTAC
ATGGAGTATGGCTATCACCTTACCAAAGCTTTCTGTTTTATCTGATATGATCAAACCATTATTGAAACATTATTTGAAAA
CCTCCGAAACTACGATGGAAAAAATCACTATCCAAAAATGTGTGGCAGATTTGAAATATCTGCCATTAGGGACCTCACCA
CTGCCTATGATGACAGCCAACCTGATAAAAAGGCTGTTCTTCCCACGAGTAAAAGCAGCCAAATGATAACATTCACCTTT
GCCAATGGAGGAGTGGCCACCATGCGAACCAGTGGGACTGAGCCCAAAATCAAGTACTACACAGAACTGTGTGCCCCTCC
TGGAAACAGTGACCCTGAGCAGCTGAAGAAGGAACTGAATGAACTAGTCAGTGCGATTGAAGAACATTTTTTCCAGGCAC
AAAAGTACAATTTG
ORF - retro_tsyr_2119 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.93 % |
| Parental protein coverage: | 82.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LTAAVLLAKDVPVYLFSRYVPTP-FVPYAVQELKAVAGVMITASHNRKEDNGYKVYWETGAQITSPHDKE |
| L.A........PVYLFS...PTP.FVPY.V..LK..AG.M.TASHN.K.DN.YKVYW..GAQI.SPHDK. | |
| Retrocopy | LAATMFISQGIPVYLFSGITPTP<FVPYTVSHLKLCAGIMDTASHNPKQDNSYKVYWDKGAQIISPHDKG |
| Parental | ILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKICFYRELNSKTTLKFVHTSFHGVGHD |
| I...IEE..EPW...W.D...D.SPL..DP...I...Y.EDLKK.CF.R..N..T..KFVHT..HGVGH. | |
| Retrocopy | ISQAIEENLEPWPQAWDDSSIDDSPLLHDPNASINNDYFEDLKKYCFHRSVNRETKVKFVHTFVHGVGHN |
| Parental | YVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELSLRLAEKENARIVLATDPDADRLAVA |
| .VQ.AF..F...PP..V..QKDPDPEF..VK.PNPEEG..VL..S...A.K....IVLA.DPDADRLAVA | |
| Retrocopy | FVQSAFKAFDLVPPEAVSKQKDPDPEFPRVKYPNPEEGKGVLTSSFAFADKTKTKIVLANDPDADRLAVA |
| Parental | ELQENGHWKVFTGNELAALFGWWMFDCWR-KNKPRNADVKNIYMLATTVSSKILKAIAFKEGFHFEETLP |
| E.Q..G.W.VF.GNEL.AL.GWW.F..W..KNK.R.A..K..YML..TVSSKIL.AIA..EGFH.EETL. | |
| Retrocopy | EKQDSGEWRVFSGNELGALLGWWLFTSWKEKNKDRSA-LKDTYMLSSTVSSKILRAIALTEGFHIEETLT |
| Parental | GFKWIGSRIKDLLENGKEVLFAFEESIGFLCGTSVLDKDGVSAAVVVAEMASYLETMNVTLKQQLIKVYE |
| GFKW.G.R.K.LL..GK.VLFAFEE..G..C...VLDKDGVSAAV..AE.AS.L.T.N....QQ....Y. | |
| Retrocopy | GFKWMGIRAKQLLDQGKTVLFAFEEAMGYMCCPFVLDKDGVSAAVIGAELASFLATKNLSMSQQRKAIYM |
| Parental | KYGYHISKTSYFLCYDPLTIKSIFERLRNFDSPKEYPKFCGTFAILHVRDITTGYDSSQPNKKSVLPVSK |
| .YGYH..K...F..YD...I...FE.LRN.D....YPK.CG.F.I...RD.TT.YD.SQP.KK.VLP.SK | |
| Retrocopy | EYGYHLTKAFCFI*YDQTIIETLFENLRNYDGKNHYPKMCGRFEISAIRDLTTAYDDSQPDKKAVLPTSK |
| Parental | NSQMITFTFQNGCVATLRTSGTEPKIKYYAEMCASPDQSDTALLEEELKKLIEALIENFLQPSKNGL |
| .SQMITFTF.NG.VAT.RTSGTEPKIKYY.E.CA.P..SD...L..EL..L..A..E.F.Q..K..L | |
| Retrocopy | SSQMITFTFANGGVATMRTSGTEPKIKYYTELCAPPGNSDPEQLKKELNELVSAIEEHFFQAQKYNL |
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_2119 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,
|