RetrogeneDB ID: retro_chof_2328

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_66273:8819..9544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG1
• Ensembl ID: ENSCHOG00000012656
• Aliases: None
• Description: BCL2-associated athanogene [Source:HGNC Symbol;Acc:937]

Sequence

>retro_chof_2328
GGCCACGGGGAGCGGCGGAGCCCCTTGCGCCTCGCCCTTGGGTGGGGCAGGGAGCCACGCAGAACAGGAGCTCCGGCCAA
GCTCGGCCAGCTCCCCTCTTAGCGTCTTCCCAACCAGAGTGGGGCCAGCAGGCATGGCCGAGCCAGCAGGAGCACCGCAA
CCGGCGCTTGCAAGCCGCGGGTAAAGAAGAAAGTCCATCCCTGCTCCATCCGGAGCTAGGAGATAGCCCAGAGCGATGAT
AATGCAGCGGGTGGGCTCAGCGTGACAGTCACCCACAGAAATGACAAGCACAACATTCATGTTACCCGGCAGCAAGGTTG
CAATGAACCGATTGTCCAAGACCTGGCCCAGCTTGTTTAAGAGACCACAGCAGTTCCACTGCATTTTCAGAAACTCGTAT
TTAAGGAAAAAATCTCTGAAGAAAATGTCAGGACTTGGAATACAAAATGGTTGCGGGTCATGCTAATTGGGAGAAAAAGA
ACAGTCCGGAGGCAGAGGTGGAATTAAAGAAGCTGAAAGATGTGGAGAACTCTGTGGAGAAGATAGGTGACCAACTGGAA
GGGGTGAATAAAGAACTCACTGGAATCCAGCAAGGTTTTCTGGCCAAGGATTTGCAAACTGAAGCTCTCAGTAAACTTGA
TAGGAGCGTAAAAGCAATAACCAAGCAGTTAATGAAGATCTTGGAGGAGATTTGCACACTAATTCTGCTAGAAAATTTCG
AAGAC

Alignment

ORF - retro_chof_2328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.59 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQGDRRVPRRLALRSGREPRQPVLPAEPGQLPFQRPPSRSGASGHDRSTRSTAAGACRPRVKKKVRPRAT
          G.G.RR.P.RLAL..GREPR....PA..GQLP..R.P..SGAS.H.R..RSTA.GAC.PRVKKKV.P...
Retrocopy GHGERRSPLRLALGWGREPRRTGAPAKLGQLPS*RLPNQSGASRHGRASRSTATGACKPRVKKKVHPCSI

Parental  RSEEMARSEDMAAG-VNVTVTHSNEKHDLHVTPQQGYSEPVVQDLAQVVEETTGVPLPFQKLIFKG-KSL
          RS.E.A.S.D.AAG...VTVTH.N.KH..HVT.QQG..EP.VQDLAQ.V.ETT.VPL.FQKL.FK..KSL
Retrocopy RS*EIAQSDDNAAGGLSVTVTHRNDKHNIHVTRQQGCNEPIVQDLAQLV*ETTAVPLHFQKLVFKE>KSL

Parental  KEMEQPLSALGIQNGCRVMLIG-KKNSPEEEAELKKLKDLEESVES-SNQLEA-DKELTGIQQGFLAKDL
          K......S.LGIQNGC.....G.KKNSPE.E.ELKKLKD.E.SVE....QLE...KELTGIQQGFLAKDL
Retrocopy KK----MSGLGIQNGCGSC*LG>KKNSPEAEVELKKLKDVENSVEKIGDQLEGVNKELTGIQQGFLAKDL

Parental  QAEALAKLDRRVKATIEQFMKILEEIDTLVLPENFKD
          Q.EAL.KLDR.VKA...Q.MKILEEI.TL.L.ENF.D
Retrocopy QTEALSKLDRSVKAITKQLMKILEEICTLILLENFED

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_2328 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017845	1 retrocopy	retro_btau_901,
Choloepus hoffmanni	ENSCHOG00000012656	1 retrocopy	retro_chof_2328 ,
Callithrix jacchus	ENSCJAG00000008074	1 retrocopy	retro_cjac_4052,
Equus caballus	ENSECAG00000017942	1 retrocopy	retro_ecab_267,
Homo sapiens	ENSG00000107262	1 retrocopy	retro_hsap_4673,
Gorilla gorilla	ENSGGOG00000016534	1 retrocopy	retro_ggor_2899,
Macaca mulatta	ENSMMUG00000020148	1 retrocopy	retro_mmul_2487,
Nomascus leucogenys	ENSNLEG00000005204	1 retrocopy	retro_nleu_2165,
Oryctolagus cuniculus	ENSOCUG00000008945	1 retrocopy	retro_ocun_481,
Pongo abelii	ENSPPYG00000019138	1 retrocopy	retro_pabe_3630,
Pan troglodytes	ENSPTRG00000020856	1 retrocopy	retro_ptro_3105,
Tursiops truncatus	ENSTTRG00000010573	2 retrocopies	retro_ttru_252, retro_ttru_946,