RetrogeneDB ID: retro_chof_329

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7422:15725..15949(-)
• Located in intron of: ENSCHOG00000007264

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL1
• Ensembl ID: ENSCHOG00000001218
• Aliases: None
• Description: GABA(A) receptor-associated protein like 1 [Source:HGNC Symbol;Acc:4068]

Sequence

>retro_chof_329
TTCATGTATAAAGAGTAGCATTCTTTAAAGAAGCACCGTTCTGAGGCCAAGTAAATATGAAAGAAATACCCACAACAGGT
CATAGTGACAGTAGAGAAGGTTACCAAAATTCAGATGGGAGACCTGGGCAAAATGAAATACCTGGTACCTTCTGATCTCA
CAGTTGGCCAGTTCTTTGTCTTGATTAGAAACAGATTCATCTCCAAGCTTAGGATGCCTTGTTT

Alignment

ORF - retro_chof_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 64.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FQYKEDHPFEYRKKEGEKIRKKYPDRVPXXXXXAPKARVPDLDKRKYLVPSDLTVGQFYFLIR-KRIHLR
          F.YKE.H.......E...I.KKYP..V........K....DL.K.KYLVPSDLTVGQF..LIR.K.IHL.
Retrocopy FMYKE*HSLKKHRSEAK*I*KKYPQQVIVTVEKVTKIQMGDLGKMKYLVPSDLTVGQFFVLIR<KQIHLQ

Parental  PEDALF
          ..DALF
Retrocopy A*DALF

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_329 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001218	1 retrocopy	retro_chof_329 ,
Choloepus hoffmanni	ENSCHOG00000012090	7 retrocopies	retro_chof_146, retro_chof_2230, retro_chof_2274, retro_chof_2432, retro_chof_510, retro_chof_558, retro_chof_960,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,