RetrogeneDB ID: retro_chof_556

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_121125:702..1317(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSCHOG00000002028
• Aliases: None
• Description: COP9 signalosome subunit 5 [Source:HGNC Symbol;Acc:2240]

Sequence

>retro_chof_556
GTTGGCCACCTTGAAAATGCAATTTTCTGGTATCATAGCTATGGCTGCTCGCTTTCTGGGATTGATGTTAGTACTCAGAT
GCTCAATCATCAGTTCCAGGAATCATTTGTAGCAGTGGAAATTGACCCAACAAGAACAATATCTGCAGGGAAAGTGAATC
TTGATGCCTTTAGGACATACCCAAAGGGCTACAAAGCACCTGAGGAAGTATCTTCTGAGTACCAGATTATACCACTTAAT
AAGATAGAAGACTTTGGTGTACACTGCAAACAATGTTATGCCTTGGAAGTCTCATATTTCATATCCTCTTTGGACTGCAA
ATTGCTTGAGCTTTTATGGAATAAATACTGGGTGAATACGCTGAGTTCTTCTACCTTGCTTACTAACGCAGACTACACCA
CTGATCAGGTCTTTGATTTCTCTGAGAAGTTAGAGCAGTCAGAAGCCCAGCTGGGACAAGGGAGTTTTACGTTGGGTTTG
GAAAAACATTACTGAAAGTCAGAAGACAAATTTGCCAAAGCTACGTGAGACAGCTATAAAACCACCATAGAAGCTATCCA
TTGATTGATGTCTCAGGCTATTAAGGATAAACTATTTAATCAAATTAATATCTCT

Alignment

ORF - retro_chof_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.21 %
• Parental protein coverage: 69.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPP
          VG.LENAI.WYHS...YGC.LSGIDVSTQMLN.QFQE.FVAV.IDPTRTISAGKVNL.AFRTYPKGYK.P
Retrocopy VGHLENAIFWYHS---YGCSLSGIDVSTQMLNHQFQESFVAVEIDPTRTISAGKVNLDAFRTYPKGYKAP

Parental  DEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTPSSSSLF-NADYTTGQV
          .E..SEYQ.IPLNKIEDFGVHCKQ.YALEVSYF.SSLD.KLLELLWNKYWVNT.SSS.L..NADYTT.QV
Retrocopy EEVSSEYQIIPLNKIEDFGVHCKQCYALEVSYFISSLDCKLLELLWNKYWVNTLSSSTLLTNADYTTDQV

Parental  FDLSEKLEQSEAQLGRGSFMLGLGTHDRKSED-LAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINVS
          FD.SEKLEQSEAQLG.GSF.LGL..H..KSED..AKAT.DS.KTTIEAIH.LMSQ.IKDKLFNQIN.S
Retrocopy FDFSEKLEQSEAQLGQGSFTLGLEKHY*KSEDKFAKAT*DSYKTTIEAIH*LMSQAIKDKLFNQINIS

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_556 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002028	1 retrocopy	retro_chof_556 ,
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454,
Myotis lucifugus	ENSMLUG00000011697	1 retrocopy	retro_mluc_1528,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Tupaia belangeri	ENSTBEG00000008440	7 retrocopies	retro_tbel_1083, retro_tbel_1833, retro_tbel_1853, retro_tbel_2528, retro_tbel_3147, retro_tbel_3896, retro_tbel_3914,