RetrogeneDB ID: retro_cjac_3041

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:155678476..155679293(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSCJAG00000007908
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_cjac_3041
GCTGCAAGGCCTCATTCCATTGATGGGAGAGTCCTTGAACCAAAACGTGCTGTAGCAGGAGAGGAATCTGGAAAACCGGG
GGCTCATGTAACTGTGAAGAAGCTGTTTGTTGGTGGAATTAAGATACTGAGGAACGTCACCTTAGAGATGACTTTGAGGA
GTATGGAAAGATCGATACCATTGAAATAATTACTGATAGGCAGTCTGGAAAGAAGAGAGGCTTTGGCTTGGTTACTTTGA
TGACCATGATCCTGCGGATAAAATCGTGTTGCGGAAATACCACAGCATCAGTGGTCCTAATGCAGAAGGAAGAAAGGCTC
TGTCTAGACAAGAAATGCAGGAACTTCAAAGTTCTAGGAGTGGAAGAGGAGGCAGCTTTGGCTTTCGGGATTCTCGTAGC
GGTGGAGGAAATTTCGGACCAGGACCAGGAAGTAACTTTAGAGGAGGAGCTGATGGATATGGCAGTGGACGTGGATTTGG
GGATGGCTACAGTGGGTATGGAGGAGGACCCGGAGGTGGCAATTTTGGAGGTAGCCCTGGTTATGGAGGAGGCAGAGGAG
GATATGGTGGTGGGGGACCTGGATATGGCAACCAGGGTGGGGGCTACAGAGGTGGTTATGACAACTATGGAGGAGGAAAT
TATGGCAGCGGAAATTACAATGATTTTGGAAATTATAACCAGCAACCTCCTAACTACGGTCCAATGAAAAGTGGAAACTT
TGGTGGCAGCAGGGACATGGGGGGACCATATGGTGGAGGAAACTATGGTCCAGGAGGCAGTGGAGGAAGGGGGGGTTATG
GTGGGAGGAGCCGATAT

Alignment

ORF - retro_cjac_3041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIK-EDTEEHHLRDYFEEYGKIDTIEIITDRQ
          AARPHSIDGRV.EPKRAVA.EESGKPGAHVTVKKLFVGGIK....E.H.LRD.FEEYGKIDTIEIITDRQ
Retrocopy AARPHSIDGRVLEPKRAVAGEESGKPGAHVTVKKLFVGGIK<DTEERH-LRDDFEEYGKIDTIEIITDRQ

Parental  SGKKRGFGFVT-FDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGGG
          SGKKRGFG.VT.FDDHDP.DKIVL.KYH.I.G.NAE.RKALSRQEMQE.QSSRSGRGG.FGF.DSR.GGG
Retrocopy SGKKRGFGLVT<FDDHDPADKIVLRKYHSISGPNAEGRKALSRQEMQELQSSRSGRGGSFGFRDSRSGGG

Parental  NFGPGPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYGGGY
          NFGPGPGSNFRGG.DGYGSGRGFGDGY.GYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGY.GGY
Retrocopy NFGPGPGSNFRGGADGYGSGRGFGDGYSGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYRGGY

Parental  DNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGGSGGSGGYGGRSRY
          DNYGGGNYGSGNYNDFGNYNQQP.NYGPMKSGNFGGSR.MGGPYGGGNYGPGGSGG.GGYGGRSRY
Retrocopy DNYGGGNYGSGNYNDFGNYNQQPPNYGPMKSGNFGGSRDMGGPYGGGNYGPGGSGGRGGYGGRSRY

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	0.00 RPM	127.82 RPM
SRP051959_heart	0.00 RPM	138.32 RPM
SRP051959_kidney	0.07 RPM	169.99 RPM
SRP051959_liver	0.15 RPM	141.68 RPM
SRP051959_lung	0.02 RPM	198.28 RPM
SRP051959_lymph_node	0.02 RPM	274.21 RPM
SRP051959_skeletal_muscle	0.02 RPM	132.38 RPM
SRP051959_spleen	0.00 RPM	217.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3041 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3041 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis	ENSCING00000004062	1 retrocopy	retro_cint_7,
Callithrix jacchus	ENSCJAG00000007908	2 retrocopies	retro_cjac_2285, retro_cjac_3041 ,
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Rattus norvegicus	ENSRNOG00000011175	3 retrocopies	retro_rnor_1824, retro_rnor_2043, retro_rnor_2339,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,