RetrogeneDB ID: retro_chof_1710

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_365005:467..898(-)
• 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_1710
CAGAAGAAGTGCCCATCCATGCCCAGTGAGGAACTTTGAGATTGCATCCAAAAGACTTTGAATGAGTGGAATTCCCAAAT
CAGCCCAGATTTGGTCAGGGAGTTTCCAGATGTCTTGGAATGTCTGTATCTTATGCAGTAGAAAAGATAAATCATGGTGA
GGGAGAAGAAATGAAAGTTTCTGCAAAACTGTTCATTGTAGGATCAAACTCTTCATCATCAACTAGAAATGCAGCTGAGA
TGGCCTGTTCAGTCCTTGGAGTTGCACAGCTAGATTCTGTGATCATTGTTTCACCTCCTGTTGAAGATGGAGTTAATCTT
TCTTTGGAGCATTTGCAGCCTAAATGGGAGGAATTGGAAAACTTAGTTCAGAACAAACAGATTGTTGCTGTCAGTACCTC
TGGTCTAGATTAAACAGAGTTGGAGCAGCTG

Alignment

ORF - retro_chof_1710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.45 %
• Parental protein coverage: 59.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKKCPSTHSEELRDCIQKTLNEWSSQISPDLVREFPDVLEC-TASHAVEKINPDEREEMKVSAKLFIVGS
          .KKCPS..SEEL.DCIQKTLNEW.SQISPDLVREFPDVLEC...S.AVEKIN..E.EEMKVSAKLFIVGS
Retrocopy QKKCPSMPSEEL*DCIQKTLNEWNSQISPDLVREFPDVLEC<SVSYAVEKINHGEGEEMKVSAKLFIVGS

Parental  NSSSSTRNAVDMACSVLGVAQLDSV-IASPPIEDGVNLSLEHLQPYWEELENLVQNKKIVAIGTSDLDKT
          NSSSSTRNA..MACSVLGVAQLDSV.I.SPP.EDGVNLSLEHLQP.WEELENLVQNK.IVA..TS.LD.T
Retrocopy NSSSSTRNAAEMACSVLGVAQLDSVIIVSPPVEDGVNLSLEHLQPKWEELENLVQNKQIVAVSTSGLD*T

Parental  QLEQL
          .LEQL
Retrocopy ELEQL

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_1710 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 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,