RetrogeneDB ID: retro_chof_2594

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_89135:2679..3629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEH1L
• Ensembl ID: ENSCHOG00000000545
• Aliases: None
• Description: SEH1-like (S. cerevisiae) [Source:HGNC Symbol;Acc:30379]

Sequence

>retro_chof_2594
GTCTGGTATAAAAGTGAAAGTGGAGATTGGCATTTTCCTGCTGGTTGGAAGATGTATAGTGGCTCTGTGTGGCATGTGAC
ATGGGCCCATCCTGAGTTTGGACAGGTTTTAGCTTCCTGTTTCTTTGACCGAACAGCAGCTGTTTGGGAAGAAATATGAG
GAGACTCGAATCACAAACTGCAAGGACAGAGTCACTGGGTGAAGAGAACAACTTTAGCAGATAGCAGAACATCAGTTACC
AATGTGAAATTTGTTCCCAGGCATATGGGTATTATGTCGGCAACCTGTTCAGCGGATGGTATCCTAAGAATATACGAGGC
ACCCGATGTTATGAACCTCAGTCAGTGGTCTCTGCAGCAGAGATGTCATGCAAGCTGAGCTGTAGCTGTATTTCCTGGAA
CCCTTCAAGCTCCCATGCCATTCTCCCATGAGAGCTGTAAGAAGGGATGACAGTGGCCCAAATGCAATGGCCAAGGTGCA
GATTTTTGAACATAATGAAAACACCAGGAAATTTGCAAAAGCAGAAACACTTATGACCGTCACTGATTCTATGCCTGATA
TTTCATTTGCTCTGAATTTGGGAAGGTCTTTGACATTCTAGCTAAAGCAACAAAAGATGTGAGGATTTTTACTCTAAAAC
CTGTGAGCAAAGAATTGAATTCCTCTGGTGGGCCAACAGAATTCAAAATCCATGTAGTGGCTCAGTTTGATAACCATAAT
TCCCAGGTCTGGAGAGTGAGTTGGAATGTAATGGAAACAGTCCTGGCATCTTCAGGAGATGGTGGCTGTGTGAGATTGTG
AAAGCCAATTACATCGACAACTGGAAGTGCACTGATCTGAAAGATAACGGGACCCCCGTCAGTGGGAGTTCCCAGCATGG
AAACTCAAACCTTTCCCTAGGCTCAAATGTTCCAAATCTACAAAATTCATCACGTGGACCTTCTGCTGGC

Alignment

ORF - retro_chof_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 84.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VWDKSESGDWHCTASWKTHSGSVWRVTWAHPEFGQVLASCSFDRTAAVWEEIVGESNDKLRGQSHWVKRT
          VW.KSESGDWH..A.WK..SGSVW.VTWAHPEFGQVLASC.FDRTAAVWEEI.G.SN.KL.GQSHWVKRT
Retrocopy VWYKSESGDWHFPAGWKMYSGSVWHVTWAHPEFGQVLASCFFDRTAAVWEEI*GDSNHKLQGQSHWVKRT

Parental  TLVDSRTSVTDVKFAPKHMGLMLATCSADGIVRIYEAPDVMNLSQWSLQH-EISCKLSCSCISWNPSSSR
          TL.DSRTSVT.VKF.P.HMG.M.ATCSADGI.RIYEAPDVMNLSQWSLQ..E.SCKLSCSCISWNPSSS.
Retrocopy TLADSRTSVTNVKFVPRHMGIMSATCSADGILRIYEAPDVMNLSQWSLQQ<EMSCKLSCSCISWNPSSSH

Parental  A-HSPMIAVGSDDSGPNAMAKVQIFEYNENTRKYAKAETLMTVTDPVHDIAFAPNLGRS-FHILAIATKD
          A.HSPM.AV..DDSGPNAMAKVQIFE.NENTRK.AKAETLMTVTD...DI.FA.NLGRS.F.ILA.ATKD
Retrocopy A<HSPMRAVRRDDSGPNAMAKVQIFEHNENTRKFAKAETLMTVTDSMPDISFALNLGRS<FDILAKATKD

Parental  VRIFTLKPVRKELTSSGGPTKFEIHVVAQFDNHNSQVWRVSWNITGTVLASSGDDGCVRL-WKANYMDNW
          VRIFTLKPV.KEL.SSGGPT.F.IHVVAQFDNHNSQVWRVSWN...TVLASSGD.GCVRL..KANY.DNW
Retrocopy VRIFTLKPVSKELNSSGGPTEFKIHVVAQFDNHNSQVWRVSWNVMETVLASSGDGGCVRL<VKANYIDNW

Parental  KCTGILKGNGSPVSGSSQQGNANPSLGSNVPNLQNSLHGPSAG
          KCT..LK.NG.PVSGSSQ.GN.N.SLGSNVPNLQNS..GPSAG
Retrocopy KCTD-LKDNGTPVSGSSQHGNSNLSLGSNVPNLQNSSRGPSAG

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_2594 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000545	2 retrocopies	retro_chof_165, retro_chof_2594 ,
Oryctolagus cuniculus	ENSOCUG00000006858	2 retrocopies	retro_ocun_1723, retro_ocun_1801,
Sus scrofa	ENSSSCG00000030252	2 retrocopies	retro_sscr_178, retro_sscr_186,