RetrogeneDB ID: retro_chof_1528

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31607:14692..15354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCLY
• Ensembl ID: ENSCHOG00000013824
• Aliases: None
• Description: selenocysteine lyase [Source:HGNC Symbol;Acc:18161]

Sequence

>retro_chof_1528
AGAAAGGCCAAGGATATCATAAGGGCAGCTAGGGAGAACCTGGCGAAGATGATCAGCAGAGAACCTCAAGACATAATCTT
CACATCTGGAGGTACCGAGTCAAATAACTTAGTAATCCATTCTGCGGTGAAACACTTCCATGAAAACCAAGCCTCCTGAG
AAGACAAGGCTGAGTGTCACAAGCCCCATTTTATCACCTCCACCGTGGAGCGTGATTCGTCTGGCTGCCCCTGGCGCACC
TGGTGAAGGAGGACATGGCCGCTGTCACCTTTGTCTTGGTGTCCAAGGTGAGTGGGCAGGTAGAAGTGGATGATGTCCTG
GCGGCAGTGCACCCCACCACGTGCCTAGTGACCGTCATGCTGGCCAACAACAAGACGGGCGTGATCATGCCCGTCTCTGT
CATCAGCCAGCGCGTCAAGGCCTTGAACTGGAGGTGGGCCACGTCAGGGCTGCCCCCTGTCCTGGTGCACAGGGATGCCG
CACAGGCCCTGGGCAAGAGACGTGTGGACATGGAGGACTTGGACATGGACTTCCTCACCATCGTGGGGTACAAGTTCTGT
GGTCCCAGGATTGGAGCACTTTATGTGTGAGGGCTGGTTGAACTCACCCCTCTGTACCCCATGCTGTTTGGAGGTGGGCA
GGAGCAGCACTTCAGACCTGGG

Alignment

ORF - retro_chof_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.58 %
• Parental protein coverage: 68.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKAKDIIRAARENLAKMISGEPQDIIFTSGGTESNNLVIHSVVKHFQENQTSREDKTEHHKPHFITSTVE
          RKAKDIIRAARENLAKMIS.EPQDIIFTSGGTESNNLVIHS.VKHF.ENQ.S.EDK.E.HKPHFITSTVE
Retrocopy RKAKDIIRAARENLAKMISREPQDIIFTSGGTESNNLVIHSAVKHFHENQAS*EDKAECHKPHFITSTVE

Parental  HDS-VRLPLEHLVNEDVAAVTFVSVSEVSEWAGVEEN-AAVRLRTEVVPFKI-NNETASIMPVPAISQRV
          .DS.V.LPL.HLV.ED.AAVTFV.VS.VS....V....AAV...T..V.....NN.T..IMPV..ISQRV
Retrocopy RDS<VWLPLAHLVKEDMAAVTFVLVSKVSGQVEVDDVLAAVHPTTCLVTVMLANNKTGVIMPVSVISQRV

Parental  KALNQRRAAVGLPPVLVHTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYVRGLGELTPLHPML
          KALN.R.A..GLPPVLVH.DAAQALGKRRVD.EDL..DFLTIVG.KF.GPRIGALYV.GL.ELTPL.PML
Retrocopy KALNWRWATSGLPPVLVHRDAAQALGKRRVDMEDLDMDFLTIVGYKFCGPRIGALYV*GLVELTPLYPML

Parental  FGGGQERHFRPG
          FGGGQE.HFRPG
Retrocopy FGGGQEQHFRPG

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_1528 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013824	2 retrocopies	retro_chof_1528 , retro_chof_1707,
Callithrix jacchus	ENSCJAG00000000471	1 retrocopy	retro_cjac_3989,
Oryctolagus cuniculus	ENSOCUG00000002777	1 retrocopy	retro_ocun_405,
Tarsius syrichta	ENSTSYG00000002756	1 retrocopy	retro_tsyr_1779,