RetrogeneDB ID: retro_chof_765

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_144830:4841..5488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GCLM
• Ensembl ID: ENSCHOG00000012122
• Aliases: None
• Description: glutamate-cysteine ligase, modifier subunit [Source:HGNC Symbol;Acc:4312]

Sequence

>retro_chof_765
ACTTTGAATGAGTGGAGTTAACAAATCAGCCCAGGTTTGGTCAGGGAATTTCCGGTTGTCTTGGAATGTACTGTATCTCA
TGCAATAGAAAAGAAAAATCCTGATGAGAGAGAAGAAATGAAAGTTTCTGCAAAACTGTTCAATGTAGGATCAAACTCTT
CATCATCAACAAGAAATGCAGTTGACGTGGCCTGTTCAGTCCTTGGAGTTGCACAACTAGATTCTGTGATCATTGCTTCA
TCTCCTATTGAAGATGGAGTTAATCTTTCCTTGAAGCATTTGCAACCTTACTGGGAGGAACTGGAAAACTTAATTCAGAA
CAAAAAGATTATTGCTATAGGTACTTCTGATTTACATAAAACACAGTTGGAGCAGCTGTATCAGCAGGCACAGGGAAAAC
CAAATAGTAACTAAGTTAATCTTGCCTGCTACTATGTGATGCCACCTGATTTGAGTGCATTTGCTAAACAATTTGACATA
CAGCTATTGACTCACAATGATAAAAAGAACTGCTTTCTAAAGTAAGTTTCCAAGAAGCTCTTCAGGAAAGCATCCCTGGC
ATTCAAGCACATGAGTGGGTACCACTATGGCTTCTGTGATTTTCAGTGATTGTTAAAAGTAGAGGAATTATCGAATCAAA
AGGCTAC

Alignment

ORF - retro_chof_765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 88.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLNEWSSQISPDLVREFPDVLECTASHAVEKINPDEREEMKVSAKLFIVGSNSSSSTRNAVDMACSVLGV
          TLNEWS.QISP.LVREFP.VLECT.SHA.EK.NPDEREEMKVSAKLF.VGSNSSSSTRNAVD.ACSVLGV
Retrocopy TLNEWS*QISPGLVREFPVVLECTVSHAIEKKNPDEREEMKVSAKLFNVGSNSSSSTRNAVDVACSVLGV

Parental  AQLDSVI-ASPPIEDGVNLSLEHLQPYWEELENLVQNKKIVAIGTSDLDKTQLEQLYQWAQVKPNSNQVN
          AQLDSVI.AS.PIEDGVNLSL.HLQPYWEELENL.QNKKI.AIGTSDL.KTQLEQLYQ.AQ.KPNSN.VN
Retrocopy AQLDSVIIASSPIEDGVNLSLKHLQPYWEELENLIQNKKIIAIGTSDLHKTQLEQLYQQAQGKPNSN*VN

Parental  LASCCVMPPDLTAFAKQFDIQLLTHNDP-KELLSEASF-EALQESIPDIQAHEWVPLWLLRYSVIVKSRG
          LA...VMPPDL.AFAKQFDIQLLTHND..KELLS..SF.EALQESIP.IQAHEWVPLWLL..SVIVKSRG
Retrocopy LACYYVMPPDLSAFAKQFDIQLLTHNDK<KELLSKVSFQEALQESIPGIQAHEWVPLWLL*FSVIVKSRG

Parental  IIKSKDY
          II.SK.Y
Retrocopy IIESKGY

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_765 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012122	2 retrocopies	retro_chof_1710, retro_chof_765 ,
Tupaia belangeri	ENSTBEG00000006631	1 retrocopy	retro_tbel_3522,