RetrogeneDB ID: retro_pabe_3630

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:39002782..39003329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG1
• Ensembl ID: ENSPPYG00000019138
• Aliases: None
• Description: BCL2-associated athanogene [Source:HGNC Symbol;Acc:937]

Sequence

>retro_pabe_3630
AGCGAGAAGGTGACCAAGGAGGAAATGGTGGCAGCCAAGCTCAGCATGACTGTCACTCACAGCAATGAGAAGCATGACCT
TCGCGTTACCCTGCAGCAGGTCCAGTGGTGAACCAATTGCCCAAGACCTGACCCAGGTTGTTGGAGAGGCCCCAGGGGTT
CCACTGTCTTTTCAGAAACTCATATTTAAGGGAACATCTCTGAAGGAAATGGAGATACCTTTGTCAGCATGTGGAATACA
AAATGGTTGCCAAGTCATGTTAATTGGGAAAAAGAACAGTCCAGAGGAAGAGGTTGAACTGGAGAAATTGAAAGATTTGG
TGAAGCCTGTGGAGAAGGAAGCTGACGAACTGTAAGAGTTGAATAAACAGCTTACTGGACTCCAGCAAGGTTTTCTGGCC
AAGGATTTGCAAACTGAAGCTCTCTGCAAACTTGATAGGAGTGGAAAAGCCACAACCAAATAGTTTATGAAGATCTTGGA
AGAGATCGACACACTGATCCTGCCAGAAAATTTCAAAGACAATAGATCAAAAAGGAAAGGTTTGGTT

Alignment

ORF - retro_pabe_3630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.86 %
• Parental protein coverage: 52.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEEVTRKEMAAAGLTVTITHSNEKHDLHVTPKQ-GSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKE
          SE.VT..EM.AA.L..T.THSNEKHDL.VT..Q..S.EP..QDL.QVV.E..GVP.SFQKLIFKG.SLKE
Retrocopy SEKVTKEEMVAAKLSMTVTHSNEKHDLRVTLQQ>SSGEPIAQDLTQVVGEAPGVPLSFQKLIFKGTSLKE

Parental  METPLSALGIQDGCRVMLIGKKNSPQEEVELKKLKHLEKSVEKIADQLEELNKELTGIQQGFLPKNLQAE
          ME.PLSA.GIQ.GC.VMLIGKKNSP.EEVEL.KLK.L.K.VEK.AD.L.ELNK.LTG.QQGFL.K.LQ.E
Retrocopy MEIPLSACGIQNGCQVMLIGKKNSPEEEVELEKLKDLVKPVEKEADEL*ELNKQLTGLQQGFLAKDLQTE

Parental  ALCKLDRRVKATIEQFMKILEEIDTLILPENFKDSRLKRKGLV
          ALCKLDR..KAT...FMKILEEIDTLILPENFKD.R.KRKGLV
Retrocopy ALCKLDRSGKATTK*FMKILEEIDTLILPENFKDNRSKRKGLV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	96.43 RPM
SRP007412_cerebellum	0.00 RPM	83.42 RPM
SRP007412_heart	0.00 RPM	40.37 RPM
SRP007412_kidney	0.00 RPM	78.52 RPM
SRP007412_liver	0.00 RPM	40.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3630 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3630 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4673
Pan troglodytes	retro_ptro_3105
Gorilla gorilla	retro_ggor_2899
Macaca mulatta	retro_mmul_2487
Callithrix jacchus	retro_cjac_4052

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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,