RetrogeneDB ID: retro_chof_494

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_114671:4584..5096(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000004899
• Aliases: None
• Description: None

Sequence

>retro_chof_494
TTGAAGTCTGATCCGGCCATCTAAGCTGCCGTCGACCTCACAGAGGGGGCAAAGGGGTCACAGCACATGCGCTGACCGGG
CAGCCCTTTGACAGGATGAGAATGAAGATGCAGACGTTCCCCGACCTGTACAGCGGGCTCTCTAACTGCTGCCTCAAGAC
CTACTCCCAGGTGGGCTGCCGTGGCTTCTGCAAGGGGACCAGCCAGGCGCTGATCACCAACATCGCCGAGAACTCTGTCC
TCTTCATTTGCTACGGCTTCTGCCAACAGGTCATGAGGAACGTGGTTGGATTGGACAAGCAGGAAAAGCTGAGTGACCTA
CAGATTGTCACCACTGGCTCCTTCACCTCTGACTTTGGTGGGCTAGTGCTCTTTCCCAATGAGCTCCTGAAGTGCCGCCT
GCTGACCATGTACAAGATGGAGACATCAGGAAAGATCGCCAAAAGCCATAAGACAATTGGGTCTGACGTGAAGAGGATCC
TTGCAGAGGATGGCCAAGGGTCTCTCCAGCAC

Alignment

ORF - retro_chof_494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.19 %
• Parental protein coverage: 56.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGG-TACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFWGFYKGTSP
          .KS.PAI.AA.DLT.GA.G..TA..LTGQPFD.M..KMQTFPDLY.GL..CCLKTYSQVG..GF.KGTS.
Retrocopy LKSDPAI*AAVDLTEGAKGS<TAHALTGQPFDRMRMKMQTFPDLYSGLSNCCLKTYSQVGCRGFCKGTSQ

Parental  ALIANIAENSVLFMCYGFCQQVVRKAAGLDRQAKLSDLQNATAGSFASAFAALVLCPTELVKCRLQAMYE
          ALI.NIAENSVLF.CYGFCQQV.R...GLD.Q.KLSDLQ..T.GSF.S.F..LVL.P.EL.KCRL..MY.
Retrocopy ALITNIAENSVLFICYGFCQQVMRNVVGLDKQEKLSDLQIVTTGSFTSDFGGLVLFPNELLKCRLLTMYK

Parental  MEMSGKIAKSHNTVGSVVKSILTKDGPLGFYH
          ME.SGKIAKSH.T.GS.VK.IL..DG.....H
Retrocopy METSGKIAKSHKTIGSDVKRILAEDGQGSLQH

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_494 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494 , retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,