RetrogeneDB ID: retro_chof_641

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_129847:4485..5046(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GADL1
• Ensembl ID: ENSCHOG00000007806
• Aliases: None
• Description: glutamate decarboxylase-like 1 [Source:HGNC Symbol;Acc:27949]

Sequence

>retro_chof_641
ACTGAGAACTTTTGCCCTGTAGAAACAGATGGAAGAAGTAAAATGATAATTGAGGAACTGGAGAAGCGAGTCTGGCAAGC
TGGAAAGAAGGGGCAGCACCATTTCTTGTCTGTGACACCTCTGGTACAATTGTGTTGGGAGCCCTTGATCCTCTGGATGA
AATAACTGACATGCATGAGAGGCACAGTCTCTGGCTTCATGGGGATACTTCTTGAGGTAGCTCAGCTTTGATGTCAAGGA
AGCACTGCAAGCTTCAGCATGGCAGCCACAGGGCTGACTATGTGGCCTGGAACCCGTACAAGATGCTGATGTCTGAAATC
CAGTGCTGTACTCTTGTGAAAAAGACAAATCTGACCTTCTTAAGAAATGCTACTCAGTCAAGGCATCGTACCTCTCCAAG
GGGATAAATACTACTATGTCAGCTACAACACAGGAGACAAATCTATCCAATGTAGCAGGAGACCAGATGCATTCAAGTTC
TGAATGACCTGGAAGACCCTGGGCACATTGAGCCTTGAAGAAGGAGTTGATTGTGCTCTTGCTTTATCTAGGTACCTAGT
G

Alignment

ORF - retro_chof_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.98 %
• Parental protein coverage: 55.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TENVCFVETDGRGKMIPEELEKQVWKARK-EEAAPFLVA-TSGTTVLGAFDPLDEIADICEKHSLWLHVD
          TEN.C.VETDGR.KMI.EELEK.VW.A.K.E.AAPFLV..TSGT.VLGA.DPLDEI.D..E.HSLWLH.D
Retrocopy TENFCPVETDGRSKMIIEELEKRVWQAGK<EGAAPFLVCDTSGTIVLGALDPLDEITDMHERHSLWLHGD

Parental  ASWGGSALMSRKHRKLLHGIHRADS-ACNPH-MLMA-IQCCALLVK-DKSFLFSIKKCCSAQASYL-FQQ
          .S.G.SALMSRKH.KL.HG.HRAD..A.NP..MLM..IQCC.L..K.DKS.L...KKC.S..ASYL..Q.
Retrocopy TS*GSSALMSRKHCKLQHGSHRADYVAWNPYKMLMSEIQCCTLVKK<DKSDL--LKKCYSVKASYL<LQG

Parental  DKFYDVSYDTGDKPIQCSRRADAFKFWMTWKALGTLGLEERVNHALALSRYLV
          DK.Y.VSY.TGDK.IQCSRR.DAFKF.MTWK.LGTL.LEE.V..ALALSRYLV
Retrocopy DKYYYVSYNTGDKSIQCSRRPDAFKF*MTWKTLGTLSLEEGVDCALALSRYLV

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_641 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007806	1 retrocopy	retro_chof_641 ,