RetrogeneDB ID: retro_chof_255

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_554:16378..16860(+)
• Located in intron of: ENSCHOG00000013300

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS1
• Ensembl ID: ENSCHOG00000001139
• Aliases: None
• Description: HAUS augmin-like complex, subunit 1 [Source:HGNC Symbol;Acc:25174]

Sequence

>retro_chof_255
TCTCTCATGCTGAATGCTTTGGTTGACAGTGCAATGGCAAAGAATATGTCACTAGCTAGTTTTATCCCTGCAGTGAATGA
TTTGACCCCTGATCTTTTTTGTACCAAATCCAAAAATGAAGAAACCAAGCTTGAATTGACAGAACTTGAAAAAAGCCTAG
CTGCAACTTTAGTATTAGAAAAATGTCTACAAGAGAACCTCGGGAAGACAGAGCTGCATCTCTCTACAGAAAGGGCCAAA
GTTGACAGTTGTCTTCAGAACGTGGACTTCCTAAAAGCAAAATCAGAGGATTTCAGATTTGGAATCAAGGCTTCAGAGGA
GAACTTTCAGCCAGAGGCATGGATGCCTCTCTGTCTCATCAGCCACTGGTAGCACTGGCAGAGAAACTGGCAGAACTAAA
ATGACAGACAATACCTTTGAAGAAAAAACTGGAGTCCTATTTAGATTTAATGCTGAATCCATCTCTTGCTCAAGTGAAAA
TT

Alignment

ORF - retro_chof_255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 58.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRYLNALVDSAMTLETKDTSLASFIPAVNDLTSDLFRTKSKNEEIKLELTKLEKNLTATLVLEKCLREDV
          S..LNALVDSAM....K..SLASFIPAVNDLT.DLF.TKSKNEE.KLELT.LEK.L.ATLVLEKCL.E..
Retrocopy SLMLNALVDSAMA---KNMSLASFIPAVNDLTPDLFCTKSKNEETKLELTELEKSLAATLVLEKCLQENL

Parental  KKAELHLFTERAKVDSRLQNMDFLKAKSEEFRFGIKTAED-QLSSRGMDASLSHQSLLALSKKLAELKRQ
          .K.ELHL.TERAKVDS.LQN.DFLKAKSE.FRFGIK..E...LS.RGMDASLSHQ.L.AL..KLAELK.Q
Retrocopy GKTELHLSTERAKVDSCLQNVDFLKAKSEDFRFGIKASEE<ELSARGMDASLSHQPLVALAEKLAELK*Q

Parental  TIPLKKKLESYLDLMPNPSLAQVKI
          TIPLKKKLESYLDLM.NPSLAQVKI
Retrocopy TIPLKKKLESYLDLMLNPSLAQVKI

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_255 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 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001139	3 retrocopies	retro_chof_237, retro_chof_2496, retro_chof_255 ,
Homo sapiens	ENSG00000152240	3 retrocopies	retro_hsap_3247, retro_hsap_4075, retro_hsap_4655,
Gorilla gorilla	ENSGGOG00000010098	2 retrocopies	retro_ggor_2210, retro_ggor_2888,
Loxodonta africana	ENSLAFG00000010897	1 retrocopy	retro_lafr_1063,
Macaca mulatta	ENSMMUG00000003124	2 retrocopies	retro_mmul_2043, retro_mmul_2476,
Monodelphis domestica	ENSMODG00000003208	1 retrocopy	retro_mdom_743,
Nomascus leucogenys	ENSNLEG00000011216	3 retrocopies	retro_nleu_1091, retro_nleu_1698, retro_nleu_2043,
Pongo abelii	ENSPPYG00000009131	3 retrocopies	retro_pabe_2693, retro_pabe_3344, retro_pabe_3615,
Pan troglodytes	ENSPTRG00000009992	3 retrocopies	retro_ptro_2195, retro_ptro_2762, retro_ptro_3092,
Tupaia belangeri	ENSTBEG00000010911	4 retrocopies	retro_tbel_1209, retro_tbel_1348, retro_tbel_3868, retro_tbel_4672,