RetrogeneDB ID: retro_chof_974

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_179011:2764..3392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSCHOG00000001130
• Aliases: None
• Description: transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]

Sequence

>retro_chof_974
AGTGACAACAGCGAGCAGAACTACCACAGAACTTCTGGTTCCAGAAGTGGAAGTGCTCATGGATCTGAGAAATCTGCAGG
GCATACCCCTGCAAGGTCTCACTCCAAGGAAGATTCCAGGTGTTCCACATCAAAGCCCAGGTCCAAATATGAATCTAGGT
CTAGATCCAGAAGAATTTCTTGAAGAAATTACACAAGGTCATGGCCTCAGTACAGCTCTCATAGATGAACATGTAGCAGG
TTTTACAGTCGAGATTATCACAGACCGCATAGCCATAGTCATTCTCCAATGTCTACTCACAGGCTATGAGGTTGGAAATT
GGGCAAATCTTGATCCCATCAGTTGCCTTGGAGTATTTTGGTTGAGCTTGTACACCATAGAAAGAAATTTAAGAGAAGTG
TTCTCTAAATATGGCCCCATTGCTGACATGTCTATTGCATATGACCAGCAGTCTAGACTTCAAAAGGATTTTGCCTTTGT
GTATTTTGAAAATGTAGATGATTCCAAGGAAGCTAAAGTGTATGCCAATGAAATGGAGCTTGATGGGCATAGGATCAGAG
TTCATTTCTCTATAACTAAAAGATGGCATACCCCAACACCAGGAATTTACATGCAGAGACCTACCTAT

Alignment

ORF - retro_chof_974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.88 %
• Parental protein coverage: 75.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEVEENNFEGRESRSQSKSPTGTPARVKSESRSGSRSPSRV-SKHSESHSRSRSKSRSRSRRHSHRRYTR
          S...E.N...R.S.S.S.S..G.....KS......RS.S...S..S.S..RS...SRSRSRR.S.R.YTR
Retrocopy SDNSEQNYH-RTSGSRSGSAHGSE---KSAGHTPARSHSKEDSRCSTSKPRSKYESRSRSRRIS*RNYTR

Parental  SRSHSHSHRRRSRSRSYTPEYRRRRSRSHSPMSNRRR-HTGSRANPDPNTCLGVFGLSLYTTERDLREVF
          S.....SHR....SR.Y...Y.R..S.SHSPMS..R....G..AN.DP..CLGVF.LSLYT.ER.LREVF
Retrocopy SWPQYSSHR*TC-SRFYSRDYHRPHSHSHSPMSTHRL>EVGNWANLDPISCLGVFWLSLYTIERNLREVF

Parental  SRYGPLSGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPGIYM
          S.YGP.......YDQ.......FAFVYFE..DDSKEA...AN.MELDG.RIRV..SITKR.HTPTPGIYM
Retrocopy SKYGPIADMSIAYDQQSRLQKDFAFVYFENVDDSKEAKVYANEMELDGHRIRVHFSITKRWHTPTPGIYM

Parental  GRPTH
          .RPT.
Retrocopy QRPTY

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_974 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974 ,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,