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 symbol: PTPN4
• Ensembl ID: ENSCHOG00000001015
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) [Source:HGNC Symbol;Acc:9656]

Sequence

>retro_chof_785
TCACCAGAGATCCCTGGGGATGGGCAGCCTCCAGCTTTACCACCCAAACAATCTAAGAAAAACAGTTAGAACCAAACTCA
TTATTCACACTCTCAACAAGATCTGGAAAACCACACTAATGAAACTTTTGATGTTCCATCTTCCCCTGAAAAATCTACTC
CTACTGGTGATATTCCACATGATAATCTTGTTCTAATCAGAATGAAACCTGATGACAATGGAAGGTTTGGAGTCAATGTA
AAGGGAGGATATGATCAGAAGATGCCTGTGATTATGACCCAAGTAGCACCAGGGACACCTGCTGACCTCTGTGTCCCTCG
ATTGAATGAAGGGGACCAGGTTGTACTGATCAGTGGTCGGGACATTGCAGAACATACCCATGATCAGGAAGTCATGTTTA
TTAAAGCGAGCTGTGAGAGACATTCTGGTGAACTCATGCTCCTAGTTCAACCTAATGCTGTATATGATGTAGTGGAAGAA
AAGCTAGAAAAGGAGCCAGACCTCCAGTACATTCCTGAGAAAGCCCCAGTAGATAATGTCCATCTGGATGACTACTCCCT
GTGGAAGTCAACGATCCAGCTACCTGACGGGATTGTCACTGGAACAGTCCTAACACAATTTGATCAACTGTATTGGAAAA
AACCTGGAATGACAATGTCTTGTGCCAAATTACCTCAGAACATTTCCAAAAATATATACAGAGATATTTCACCTTATGAT
GCTACATGGGTTGTTTTAGAGGGTAATGAACACTACATCAATGCAAATCATAGAAATATGGAAATCCCTTCTTCCAGCAT
TATAAATCAGTACATTTCTTGTCAAGGCTCATTACCACACACTCATACAGATTTTTGGCAAATGACTTGGGAACAAGTTT
CCTCCATGGTTGTAATGTTGACCACACAATTTGAATGTGGAAGAGTTAAGTGTCACCAGTATTGGCCAGAACCCACAGGA
AGTTCCTCTTACAGGTGCTACCAAGTCACCTGCCACTCAGAAGAAGGAAACACTGCCCATGTATTCAGGAAGATGACACT
ATTTAACCAAGAGAAAAATGAGAGTCGTCAGCTCACTCAGATCCAGTACATAGCCTGTCCTGACCATGGGGTCCCAGATG
ACTCAAGTGACTTTCTGGATTTTGTTTGTCATGTACAAAATAAGAGGGCTGGCAAGGAAGAACCTATTGTTGTTCATTGC
AGTGCTGGGATTGGGAGAATAGGTATTCTTACTACTATGAAAACAGCCATGTGTCTCATTGAATGCAATCAGCCGGTTTA
TCCACTAGACATTGTAAGAACAATGAGAGACCAACGAGCCATGATGATCCAAACCCCTGGTCAACACAGATCTGTATGTG
AAGCTATTTTGAAAGTTTATGAAGAAGGATTTGTTAAACCCTTTATGACATCAAATAAA

Alignment

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_785 was not experimentally validated.

Homology

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	retro_mmul_2279,