RetrogeneDB ID: retro_chof_1388

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_279464:311..951(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SNX7
• Ensembl ID: ENSCHOG00000008131
• Aliases: None
• Description: sorting nexin 7 [Source:HGNC Symbol;Acc:14971]

Sequence

>retro_chof_1388
GAAAAGTTTATAGTGAAAAGAATGGTGGAACACTTTAATGATGACTTCACTGAGACACACAGGAATGCATTACATAAGTT
TTTTGAACCAAACTGCCGATCATCCAACTTTAACATTTAATGAAGACTTCAAAGTTTTTCTTACTGCACAAGCTTGGAAA
CTCTCTTCTCATAAGAAGCAAGGGTCTGGGCTGCTAAGTTGGATGGGGGAAACAGTAAGAGCTGTTGCATCCTCAATGAG
AGGATTTAAAAATCGCCCAGAGGAATTCATGGATACAGATAATTTTATTGAAACATTTAGCCAGAAAACAAACTTGATAG
GTAAAATATCACAGAATTTACATGAAAGAAAGGGAATATTTTGATGAAATGAAAGAATATGGCCCAATTCATATTCTGTG
GTTGGCATCAGAAGAGGATCCAGTAGACAACCTAAAGGTGCTGCCAGCTGCATTGGTAAATGCTGTAAGGCCACTGAAAA
ACAGGTGTCTGGACTCTCAGAAGCCCTACTTCCTGTTGTACATGAGTATGTGCATTATAGTGAAATGTTAATGGGTGCTT
TGAAAAGAAGAGACCAAATATAAGCAGAACTGGATTCCAAAGTTGAAGCTTTGAACTATAAAAAGGCACATACTGATCTG

Alignment

ORF - retro_chof_1388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.49 %
• Parental protein coverage: 73.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKFIVKGMVERFNDDFIETRRKALHKF-LNRIADHPTLTFNEDFKVFLTAQAWELSSHKKHGPGLLSRMG
          EKFIVK.MVE.FNDDF.ET.R.ALHKF.LN..ADHPTLTFNEDFKVFLTAQAW.LSSHKK.G.GLLS.MG
Retrocopy EKFIVKRMVEHFNDDFTETHRNALHKF>LNQTADHPTLTFNEDFKVFLTAQAWKLSSHKKQGSGLLSWMG

Parental  QTVRAVASSMRGVKNRPEEFMDMNNFIETFSQKINLIDKISQRIY-KEEREYFDEMKEYGPIHILWSASE
          .TVRAVASSMRG.KNRPEEFMD..NFIETFSQK.NLI.KISQ....KE.REYFDEMKEYGPIHILW.ASE
Retrocopy ETVRAVASSMRGFKNRPEEFMDTDNFIETFSQKTNLIGKISQNLH>KE-REYFDEMKEYGPIHILWLASE

Parental  EDLVDTL-KGVASCIDRCCKATEKQMSGVSEALLPVVHEYVLYSEMLMGVMKRRDQIQAELDSKVEALNY
          ED.VD.L.KG.ASCI..CCKATEKQ.SG.SEALLPVVHEYV.YSEMLMG..KRRDQI.AELDSKVEALNY
Retrocopy EDPVDNL<KGAASCIGKCCKATEKQVSGLSEALLPVVHEYVHYSEMLMGALKRRDQI*AELDSKVEALNY

Parental  RKADTDL
          .KA.TDL
Retrocopy KKAHTDL

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_1388 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031461	1 retrocopy	retro_btau_453,
Choloepus hoffmanni	ENSCHOG00000008131	2 retrocopies	retro_chof_1097, retro_chof_1388 ,
Gorilla gorilla	ENSGGOG00000023577	1 retrocopy	retro_ggor_744,
Macropus eugenii	ENSMEUG00000011320	1 retrocopy	retro_meug_1016,
Sarcophilus harrisii	ENSSHAG00000002487	1 retrocopy	retro_shar_420,
Tupaia belangeri	ENSTBEG00000000168	1 retrocopy	retro_tbel_2595,