RetrogeneDB ID: retro_cjac_4052

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:37255266..37255865(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG1
• Ensembl ID: ENSCJAG00000008074
• Aliases: None
• Description: BCL2-associated athanogene [Source:HGNC Symbol;Acc:937]

Sequence

>retro_cjac_4052
GTCGTGGCAGCCGAGCTCAGTGTGACCGTCACCCACAGCAATGAGCAGCATTATCTTCATGTTACCTGAAGCAGGACAGC
GGTGAACCAATTGCCCAAGACCTGACCCAGGTTGTTGCGAGAGGCCACAGGGGTTCCACTGTGTTTTCAGAAACCCATTT
TTAAGGGAACATCTCTGAAGGAAATGGAGATAGTTTTGTCGGCATTTGGAATACAAAATGGTTGCCAAGTCACGTTAATT
GGGAAAAAGAACAGTCCCAGAGGCAGAGGTTAGACTAAATAAATTAAAAGATTTGGAGAAGCCTGTGAAGAAAGCTGACA
AACTGTAAGAGTTGAATAAATAGCTAACTGGACTTCAGCAAGGTTTTCTGGGCAAAGATTTGCAAACTGAAGCTCTCTGC
AAACTTGATAGGAGAGGAAAAGCCACAACTAGTTTATGAAGATCTTGGAAGATCCTGATCTTGAAACTGATCCTTCCAGA
AAATTTCAAAGACAGTAGATCAAAAAGGAAAGGTTTGGTAAAAACAAGTTCAGGTGTTCATAGCTGAGTGTGGTACAGTG
GAGCTGAACATCTGCCAGGAGACCCAGCAGCTACAAACT

Alignment

ORF - retro_cjac_4052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.16 %
• Parental protein coverage: 56.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATAGLTVTVTHSNEKHDLRVT-PKQGSSEPLVQDLAQVV-EEATGVPLSFQKLIFKGKSLKEMETPLSA
          ...A.L.VTVTHSNE.H.L.VT..KQ.S.EP..QDL.QVV..EATGVPL.FQK.IFKG.SLKEME..LSA
Retrocopy VVAAELSVTVTHSNEQHYLHVT<LKQDSGEPIAQDLTQVV>REATGVPLCFQKPIFKGTSLKEMEIVLSA

Parental  LGIQDGCRVMLIGKKNS-PEEEAELKKLKHWEKSVEKIADQLEELSKELTGIQQGFLPKDLQAEALCKLD
          .GIQ.GC.V.LIGKKNS.PE.E..L.KLK..EK.V.K.AD.L.EL.K.LTG.QQGFL.KDLQ.EALCKLD
Retrocopy FGIQNGCQVTLIGKKNS>PEAEVRLNKLKDLEKPVKK-ADKL*ELNK*LTGLQQGFLGKDLQTEALCKLD

Parental  RKVKATIEQFMKILEEIDTLILPENFKDSRLKRKGLV-KKVQAFLAECDTVEQNICQETERLQS
          R..KAT..........I..LILPENFKDSR.KRKGLV.K.VQ.F.AEC.TVE.NICQET..LQ.
Retrocopy RRGKATTSL*RSWKILILKLILPENFKDSRSKRKGLV>KQVQVFIAECGTVELNICQETQQLQT

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
SRP051959_colon	0.02 RPM	8.85 RPM
SRP051959_heart	0.02 RPM	11.14 RPM
SRP051959_kidney	0.04 RPM	8.56 RPM
SRP051959_liver	0.00 RPM	9.62 RPM
SRP051959_lung	0.10 RPM	9.44 RPM
SRP051959_lymph_node	0.07 RPM	5.82 RPM
SRP051959_skeletal_muscle	1.14 RPM	18.87 RPM
SRP051959_spleen	0.04 RPM	5.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4052 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4052 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
Pongo abelii	retro_pabe_3630
Macaca mulatta	retro_mmul_2487

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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,