RetrogeneDB ID: retro_chof_2496

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_80087:4099..4933(+)
• Located in intron of: None

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_2496
ATGGAGGTGCCCTAGCAGAAAGAAGCATAGGTTGCTGCCTGGTTGAAAAAAAATATTTAGAGTTCATCTATACCACAATA
TGAGGTGAATGCACGGACCACAGAAATTTTATATTACCTTTCAGAATGCAACAAGGCCCGGGACAGGGATCTCTCCCTAG
TAATAGAGGGCTTGAAACAGAAAGCAAGCAAATATGAATCAGAAGCCAAGCATCTTCAAGACCTTCTCATGGAGAGTGTG
AATTTTTCCCCTGCCAATCTCTCTAGCATTAGTTCCAGATATCTGAATGCTTTGGTTGACAGTGCAATGGCGCTTGAAAC
AAAAGAAAACTCACCAGCTAGTTATATCCCTGCAGTGAATGATTTGACCTCTGATCTTTTTCGTACCAAATCCAAAAATG
AAGAAATCAAGCTTGAATTGACAAAACTTGAAAAAAACCTAAATGCAACTTTAGTATTAGAAAAATGTCTACGAGAGGAC
CTCGAGAAGGCAGAGCTGCATCTCTTTACAGAAAGGGCCAAAGTTGACAGTCGTCTTCAGAACATGGACTTCCTAAAAGC
AAAATCAGAGGAGTTCAGATTTGGAATCAAGACTGCAGAGGAGCAACTTTCAGCCAGAGGCATGGATGCTTCTCTGTCTC
ATCAGCCACTAGTAGCGCTGTCAGAGGAACTGGCAGAACTAAAACGACAGACGATACCTTTGAAGAAAAAAATGGAGTCC
TATTCAGATTTAATGCCGAATCCATCTCTTGCTCAAGTGAAAATGGAAGAAGCAAAATGAGAACTGGATGCCTTTGAAGC
TGGACTTACAAAGAAAATGGACATGATGGGACTG

Alignment

ORF - retro_chof_2496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAPRQKEAQVAAWLKKIFGDQPIPQYEVNPRTTEILYHLSERNKARDRDVSLIIEDLKQKASEYESEAK
          ME.P.QKEA.VAAWL........IPQYEVN.RTTEILY.LSE.NKARDRD.SL.IE.LKQKAS.YESEAK
Retrocopy MEVP*QKEA*VAAWLXXXI*SSSIPQYEVNARTTEILYYLSECNKARDRDLSLVIEGLKQKASKYESEAK

Parental  HLQDLLMESVNFSPASLSSTSSRYLNALVDSAMTLETKDTSLASFIPAVNDLTSDLFRTKSKNEEIKLEL
          HLQDLLMESVNFSPA.LSS.SSRYLNALVDSAM.LETK..S.AS.IPAVNDLTSDLFRTKSKNEEIKLEL
Retrocopy HLQDLLMESVNFSPANLSSISSRYLNALVDSAMALETKENSPASYIPAVNDLTSDLFRTKSKNEEIKLEL

Parental  TKLEKNLTATLVLEKCLREDVKKAELHLFTERAKVDSRLQNMDFLKAKSEEFRFGIKTAEDQLSSRGMDA
          TKLEKNL.ATLVLEKCLRED..KAELHLFTERAKVDSRLQNMDFLKAKSEEFRFGIKTAE.QLS.RGMDA
Retrocopy TKLEKNLNATLVLEKCLREDLEKAELHLFTERAKVDSRLQNMDFLKAKSEEFRFGIKTAEEQLSARGMDA

Parental  SLSHQSLLALSKKLAELKRQTIPLKKKLESYLDLMPNPSLAQVKIEEAKRELDAIEAELTKKMDMMGL
          SLSHQ.L.ALS..LAELKRQTIPLKKK.ESY.DLMPNPSLAQVK.EEAK.ELDA.EA.LTKKMDMMGL
Retrocopy SLSHQPLVALSEELAELKRQTIPLKKKMESYSDLMPNPSLAQVKMEEAK*ELDAFEAGLTKKMDMMGL

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_2496 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,