RetrogeneDB ID: | retro_chof_785 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_147832:2275..3694(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PTPN4 | ||
| Ensembl ID: | ENSCHOG00000001015 | ||
| Aliases: | None | ||
| Description: | protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) [Source:HGNC Symbol;Acc:9656] |
Retrocopy-Parental alignment summary:
>retro_chof_785
TCACCAGAGATCCCTGGGGATGGGCAGCCTCCAGCTTTACCACCCAAACAATCTAAGAAAAACAGTTAGAACCAAACTCA
TTATTCACACTCTCAACAAGATCTGGAAAACCACACTAATGAAACTTTTGATGTTCCATCTTCCCCTGAAAAATCTACTC
CTACTGGTGATATTCCACATGATAATCTTGTTCTAATCAGAATGAAACCTGATGACAATGGAAGGTTTGGAGTCAATGTA
AAGGGAGGATATGATCAGAAGATGCCTGTGATTATGACCCAAGTAGCACCAGGGACACCTGCTGACCTCTGTGTCCCTCG
ATTGAATGAAGGGGACCAGGTTGTACTGATCAGTGGTCGGGACATTGCAGAACATACCCATGATCAGGAAGTCATGTTTA
TTAAAGCGAGCTGTGAGAGACATTCTGGTGAACTCATGCTCCTAGTTCAACCTAATGCTGTATATGATGTAGTGGAAGAA
AAGCTAGAAAAGGAGCCAGACCTCCAGTACATTCCTGAGAAAGCCCCAGTAGATAATGTCCATCTGGATGACTACTCCCT
GTGGAAGTCAACGATCCAGCTACCTGACGGGATTGTCACTGGAACAGTCCTAACACAATTTGATCAACTGTATTGGAAAA
AACCTGGAATGACAATGTCTTGTGCCAAATTACCTCAGAACATTTCCAAAAATATATACAGAGATATTTCACCTTATGAT
GCTACATGGGTTGTTTTAGAGGGTAATGAACACTACATCAATGCAAATCATAGAAATATGGAAATCCCTTCTTCCAGCAT
TATAAATCAGTACATTTCTTGTCAAGGCTCATTACCACACACTCATACAGATTTTTGGCAAATGACTTGGGAACAAGTTT
CCTCCATGGTTGTAATGTTGACCACACAATTTGAATGTGGAAGAGTTAAGTGTCACCAGTATTGGCCAGAACCCACAGGA
AGTTCCTCTTACAGGTGCTACCAAGTCACCTGCCACTCAGAAGAAGGAAACACTGCCCATGTATTCAGGAAGATGACACT
ATTTAACCAAGAGAAAAATGAGAGTCGTCAGCTCACTCAGATCCAGTACATAGCCTGTCCTGACCATGGGGTCCCAGATG
ACTCAAGTGACTTTCTGGATTTTGTTTGTCATGTACAAAATAAGAGGGCTGGCAAGGAAGAACCTATTGTTGTTCATTGC
AGTGCTGGGATTGGGAGAATAGGTATTCTTACTACTATGAAAACAGCCATGTGTCTCATTGAATGCAATCAGCCGGTTTA
TCCACTAGACATTGTAAGAACAATGAGAGACCAACGAGCCATGATGATCCAAACCCCTGGTCAACACAGATCTGTATGTG
AAGCTATTTTGAAAGTTTATGAAGAAGGATTTGTTAAACCCTTTATGACATCAAATAAA
ORF - retro_chof_785 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.36 % |
| Parental protein coverage: | 51.14 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SPETPGDGQPPALPPKQSKKNSWNQIHYSHSQQDLENHINETFDVPSSPEKSTPNGGIPHDNLVLIRMKP |
| SPE.PGDGQPPALPPKQSKKNS.NQ.HYSHSQQDLENH.NETFDVPSSPEKSTP.G.IPHDNLVLIRMKP | |
| Retrocopy | SPEIPGDGQPPALPPKQSKKNS*NQTHYSHSQQDLENHTNETFDVPSSPEKSTPTGDIPHDNLVLIRMKP |
| Parental | DENGRFGFNVKXXXXXXXXXXXXXXXXXXXADLCVPRLNEGDQVVLINGRDIAEHTHDQIVMFIKASCER |
| D.NGRFG.NVK...................ADLCVPRLNEGDQVVLI.GRDIAEHTHDQ.VMFIKASCER | |
| Retrocopy | DDNGRFGVNVKGGYDQKMPVIMTQVAPGTPADLCVPRLNEGDQVVLISGRDIAEHTHDQEVMFIKASCER |
| Parental | HSGELVLLVRPNAVYDVVEEKLENEPDFQYIPEKATVDNVHLDDHSLRESMIQLAEGLVTGTVLTQFDQL |
| HSGEL.LLV.PNAVYDVVEEKLE.EPD.QYIPEKA.VDNVHLDD.SL..S.IQL..G.VTGTVLTQFDQL | |
| Retrocopy | HSGELMLLVQPNAVYDVVEEKLEKEPDLQYIPEKAPVDNVHLDDYSLWKSTIQLPDGIVTGTVLTQFDQL |
| Parental | YRKKPGMTMSCAKLPQNISKNRYRDISPYDATRVILKGNEDYINANYINMEIPSSS--GGIIACQGPLPH |
| Y.KKPGMTMSCAKLPQNISKN.YRDISPYDAT.V.L.GNE.YINAN..NMEIPSSS.....I.CQG.LPH | |
| Retrocopy | YWKKPGMTMSCAKLPQNISKNIYRDISPYDATWVVLEGNEHYINANHRNMEIPSSSIINQYISCQGSLPH |
| Parental | TCTDFWQMTWEQGSSMVVMLTTQVERGRVKCHQYWPEPTGSSSYGCYQVTCHSEEGNTACIFRKMTLFNQ |
| T.TDFWQMTWEQ.SSMVVMLTTQ.E.GRVKCHQYWPEPTGSSSY.CYQVTCHSEEGNTA..FRKMTLFNQ | |
| Retrocopy | THTDFWQMTWEQVSSMVVMLTTQFECGRVKCHQYWPEPTGSSSYRCYQVTCHSEEGNTAHVFRKMTLFNQ |
| Parental | EKNESRQLTQIQYIAWPDHGVPDDSSDFLDFVCHVRKKRAGKEEPIVVHCSAGIGRTGVLITMETAMCLI |
| EKNESRQLTQIQYIA.PDHGVPDDSSDFLDFVCHV..KRAGKEEPIVVHCSAGIGR.G.L.TM.TAMCLI | |
| Retrocopy | EKNESRQLTQIQYIACPDHGVPDDSSDFLDFVCHVQNKRAGKEEPIVVHCSAGIGRIGILTTMKTAMCLI |
| Parental | ECNQPVYPLDIVRTMRDQRAMMIQTPSQYRFVCEAILKVYEEGFVKPLMTSNK |
| ECNQPVYPLDIVRTMRDQRAMMIQTP.Q.R.VCEAILKVYEEGFVKP.MTSNK | |
| Retrocopy | ECNQPVYPLDIVRTMRDQRAMMIQTPGQHRSVCEAILKVYEEGFVKPFMTSNK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_785 was not experimentally validated.
Retrocopy orthology:
Choloepus hoffmanni 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001015 | 1 retrocopy |
retro_chof_785 ,
|
| Macaca mulatta | ENSMMUG00000005610 | 1 retrocopy |