RetrogeneDB ID: retro_chof_1244

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_235715:800..1872(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM57
• Ensembl ID: ENSCHOG00000000074
• Aliases: None
• Description: transmembrane protein 57 [Source:HGNC Symbol;Acc:25572]

Sequence

>retro_chof_1244
ACATTTTTATATCTGAAATTCCTGGTAGTGTGGGCACTTGTCCTCTTGGCAGATTTTGTCCTGGAGTTCAGATTTGAATA
CCTGTGGTCATTCTGGCTTTTCATCAGAAGCGTCTATGATTCCTTCAGGTACCAGGGATTGGCCTTCTCAGTATTTTTTG
TTTGTGTAGCATTCACATCAAATATAATATGTCTGCTGTTCATCCCCATACAATGGCTGTTTTTTGCTGCTAGCACATAT
GTATGGGTTCAGTACGTCTGGCACACAGAAAAGGGAGTGTGTTTGCCTACAGTGTCCCTCTGGATACTCTTTGTTTATAT
TGAAGCAGCAATTAGATTTAAAGATCTCAAAAATTTTCATGTAGACCTTTGTCGTCCATTTGCTGCCCACTGTATTGGGT
ATGCTGTGGTTACTTTGGGCTTTGGCTTCAAAAGTTATGTAAGCTACAAAATGCGATTAAGGAAGCAAAAGGAAGTGCAA
AAAGAGAATTAATTTTACATGCAGCTTCTTCAACAAGCCCTCCCTCCAGAGCAACAGATGCTACAGAAGCAGGAAAAAGG
CTGAAGAAGCAGTGAAAGGATTACCTGATATGGATTCCTCAATCCTTATACACCACAACGGAGGTATCCCAGCCAACAAA
AAACTGTCCACAACTTTGCCAGAGATAGAATACAGAGAAAAAGGGAAAGAAAAGGACAAGGAAGCCAAAAAACACAACCT
TGGAATAAATAACAACAATATTCTACAACCTGTAGACTCTAAAATCCAAGAAATCGAGTATATGGAAAACCATATCAATA
GTAAAAGATTAAATAATGATCTTGTGGGAAGTACAGAAAATCTCTTGAAAGAGGACTCATGCACTGCTTCCTCAAAAAAT
TACAAAAATGCCAGTGGAGTTGTGAACTCCTCACCTCGAAGTCACAGCGCCACAAATGGGAGCATTCCTTCCTCATCGAG
TAAAAATGAGAAGAAGCAGAAATGCACTAGCAAGAGCCCAAGTGCACACAAGGACTTAATGGAAAACTGTATTCCTAATA
ACCAGCTAAGCAAACCAGATGCACTGGTGAGG

Alignment

ORF - retro_chof_1244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.54 %
• Parental protein coverage: 56.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TFLYLKFLVVWALVLLADFV-EFRFEYLWPFWLFI-SVYDSFRYQGLAFSVFFVCVAFTSNIICLLFIPI
          TFLYLKFLVVWALVLLADFV.EFRFEYLW.FWLFI.SVYDSFRYQGLAFSVFFVCVAFTSNIICLLFIPI
Retrocopy TFLYLKFLVVWALVLLADFVLEFRFEYLWSFWLFIRSVYDSFRYQGLAFSVFFVCVAFTSNIICLLFIPI

Parental  QWLFFAASTYVWVQYVWHTERGVCLPTVSLWILFVYIEAAIRFKDLKNFHVDLCRPFAAHCIGYPVVTLG
          QWLFFAASTYVWVQYVWHTE.GVCLPTVSLWILFVYIEAAIRFKDLKNFHVDLCRPFAAHCIGY.VVTLG
Retrocopy QWLFFAASTYVWVQYVWHTEKGVCLPTVSLWILFVYIEAAIRFKDLKNFHVDLCRPFAAHCIGYAVVTLG

Parental  FGFKSYVSYKMRLRKQKEVQKENEFYMQLLQQALPPEQQMLQKQE-KEAEEAVKGLPDMDSSILIHHNGG
          FGFKSYVSYKMRLRKQKEVQKEN.FYMQLLQQALPP..Q.......K.AEEAVKGLPDMDSSILIHHNGG
Retrocopy FGFKSYVSYKMRLRKQKEVQKEN*FYMQLLQQALPP-EQQMLQKQ>KKAEEAVKGLPDMDSSILIHHNGG

Parental  IPANKKLSTTLPEIEYREKGKEKDKEAKKHNLGINNNNILQPVDSKIQEIEYMENHINSKRLNNDLVGST
          IPANKKLSTTLPEIEYREKGKEKDKEAKKHNLGINNNNILQPVDSKIQEIEYMENHINSKRLNNDLVGST
Retrocopy IPANKKLSTTLPEIEYREKGKEKDKEAKKHNLGINNNNILQPVDSKIQEIEYMENHINSKRLNNDLVGST

Parental  ENLLKEDSCTASSKNYKNASGVVNSSPRSHSATNGSIPSSSSKNEKKQKCTSKSPSAHKDLMENCIPNNQ
          ENLLKEDSCTASSKNYKNASGVVNSSPRSHSATNGSIPSSSSKNEKKQKCTSKSPSAHKDLMENCIPNNQ
Retrocopy ENLLKEDSCTASSKNYKNASGVVNSSPRSHSATNGSIPSSSSKNEKKQKCTSKSPSAHKDLMENCIPNNQ

Parental  LSKPDALVR
          LSKPDALVR
Retrocopy LSKPDALVR

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_1244 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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000074	1 retrocopy	retro_chof_1244 ,