RetrogeneDB ID: retro_chof_237

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5151:84560..85380(-)
• Located in intron of: ENSCHOG00000010845

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_237
ATGGAGGCGCCCCAGCAGGTTGCTGCCTGGTTGAAAAAAATATTTGGAGATCATCCTATTCCACAATATGAGGGAATCCA
CGGACCACAAAGATTTTATATCACCTTTCAGAATGCAACAAGGCCTGGGACAGGGATGTCTCCCTAGTAATAGAGGACTT
GAAACAGAAAGCTAGCAAATATGAATCAGAACCCAAGCATCTTCAAGACCTTCTCATGGCAAGTGTGAATTTTTCCCCTG
CCAATCTCTCTAGCACTAGTTCCAGATTTCTGAATGCTTTGGTTGACAGTGCAATGGTGTTTGAAACAAAAGATACCTCA
CTAGCTAGTTTTATCCCTGCAGTGAATGATTTGACCTCTGACCTTTTTTGTACCAAATCTAAAAATGAAGAAACGAAGCT
TGAATTGACAAAACTTGAAAAAAACCTAGCTGCAACTTTAGTATTAGAAAAATGTCTACGAGAAGACCTCAAGAAGGCAA
AGCTGCATCTCTTCACAGAAAGGGCCAAAGTTGACAGTCGTCTTCAGAACATGGACTTCCTAAAAGCAAAATCAGAGGAG
TTCAGATTTGGAATCAAGGCTGCAGAGGAGCAACTTTCAGCCAGAGGCATGGATGCTTCTCTGTCTCATCAATCACTAGT
AGCACCGTCAGAGAAACTGGCAGAACTGAAACGACAGCCAATAGCTTTGAAGAAAAAATAGAGTCCTATTTAGATTTAAT
GCCGAATCCATCTCTTGCTCAAGGGAAAACTGAAGAAGCAAAACAAGAATTGGATACCACTGAAGCTGAACTTACAAGGA
AAATGGACATGATGGGACTG

Alignment

ORF - retro_chof_237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEAPRQKEAQVAAWLKKIFGDQPIPQYEV-NPRTTEILYHLSERNKARDRDVSLIIEDLKQKASEYESEA
          MEAP.....QVAAWLKKIFGD.PIPQYE..NPRTT.ILYHLSE.NKA.DRDVSL.IEDLKQKAS.YESE.
Retrocopy MEAPQ----QVAAWLKKIFGDHPIPQYEG<NPRTTKILYHLSECNKAWDRDVSLVIEDLKQKASKYESEP

Parental  KHLQDLLMESVNFSPASLSSTSSRYLNALVDSAMTLETKDTSLASFIPAVNDLTSDLFRTKSKNEEIKLE
          KHLQDLLM.SVNFSPA.LSSTSSR.LNALVDSAM..ETKDTSLASFIPAVNDLTSDLF.TKSKNEE.KLE
Retrocopy KHLQDLLMASVNFSPANLSSTSSRFLNALVDSAMVFETKDTSLASFIPAVNDLTSDLFCTKSKNEETKLE

Parental  LTKLEKNLTATLVLEKCLREDVKKAELHLFTERAKVDSRLQNMDFLKAKSEEFRFGIKTAEDQLSSRGMD
          LTKLEKNL.ATLVLEKCLRED.KKA.LHLFTERAKVDSRLQNMDFLKAKSEEFRFGIK.AE.QLS.RGMD
Retrocopy LTKLEKNLAATLVLEKCLREDLKKAKLHLFTERAKVDSRLQNMDFLKAKSEEFRFGIKAAEEQLSARGMD

Parental  ASLSHQSLLALSKKLAELKRQTIPLKK-KLESYLDLMPNPSLAQVKIEEAKRELDAIEAELTKKMDMMGL
          ASLSHQSL.A.S.KLAELKRQ.I.LKK.K.ESYLDLMPNPSLAQ.K.EEAK.ELD..EAELT.KMDMMGL
Retrocopy ASLSHQSLVAPSEKLAELKRQPIALKK<KIESYLDLMPNPSLAQGKTEEAKQELDTTEAELTRKMDMMGL

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_237 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,