RetrogeneDB ID: retro_cjac_4164

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:52045034..52046001(-)
• Located in intron of: ENSCJAG00000000221

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP2
• Ensembl ID: ENSCJAG00000019897
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 2 [Source:HGNC Symbol;Acc:30291]

Sequence

>retro_cjac_4164
GCTAACAGTGGAAAACTGGAAAGGAAGTTTATGCAAACCTTTGTTCTGGCTCCTGAAGGATCTGTTCCAAATAAATTTCA
TGTTCACAAATGATATGTTTCGTTATGAAGAGGAAGTGTTCAGTGATTCTGAGCCTGAACTTGATGAAGAAGATGAAGTA
GAAGAGGAACAAGAAGAAAGACAACCATCTCCTGAACCTGTGCAAGAAAATGCAAACAGTGGTTACAATGAAGCTCACCC
TGTGACTAATGGCATAGAGGAGCCTTTGGAAGAATCCTCTCATGAACCTGAACCTGTGCCAGAATCTGAAACAAAGACTG
AAGAGCTGAAACCACAAGTGGAGGAGAAGAATTTAGAAGAATTAGAGAAGTCTACTCCTCCTCCTCTGGCAGAAACTGTT
TCTCTGCCACAAGAACCACCAAAGCCAAGAGTTGAAGCTAAAACAGAAGTTCAATCCCAGCCACCTCCTGTATGTGAAGA
GTGACCTAGACAACGACCTGCTTTCCCCGCTAGAGGACCGAGACCAGGCAGAGGAGATACGGAACTGAGTGACTATGACA
ACCGTAGAATAATTCACTATCCAGATAGTCATCAACTTTTTCTTGGTAACTTGCTACATGATATTGATGAAAATGAACTG
GAATAATTCTTCATGAGTTTTGGGAACGTTGTGGAACTTCATATCAATACCAAGGGTGTTGGGGAAAAGCTTCCAAATTT
TGGTTTTGTGGTTTTTGATGACTCTGAACCAGTTCAGAGAATCTTAATTGTGAAACTGATTATGTTTTGAGGGGAAGTAA
TTTAAATGTGAAAAAGAAAAAAACAAGAGCTACAAGAGAGCAAGAAACCAGAGGTGGTAGTGATGATTGGCAGGGTTATT
AGGCGCAATGATCAAGGTCCTGGTGGTCCACGTGGAATTGTGGGTGGCAGAATGATGCATGAGCATAATGGAAGAGGACC
TCCTCCA

Alignment

ORF - retro_cjac_4164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 72.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNSGQPERKFMQTFVLAPEGSVPNKFYVH-NDMFRYEDEVFGDSEPELDEESEDEVEEEQEERQPSPEPV
          .NSG..ERKFMQTFVLAPEGSVPNKF.VH.NDMFRYE.EVF.DSEPELDEE..DEVEEEQEERQPSPEPV
Retrocopy ANSGKLERKFMQTFVLAPEGSVPNKFHVH>NDMFRYEEEVFSDSEPELDEE--DEVEEEQEERQPSPEPV

Parental  QENANSGYYEAHPVTNGIEEPLEESSHEPEPEPESETKTEELKPQVEEKNLEELEEKSATPPPAEPVSLP
          QENANSGY.EAHPVTNGIEEPLEESSHEPEP.PESETKTEELKPQVEEKNLEELE.KS..PP.AE.VSLP
Retrocopy QENANSGYNEAHPVTNGIEEPLEESSHEPEPVPESETKTEELKPQVEEKNLEELE-KSTPPPLAETVSLP

Parental  QEPPKPRVEAKPEVQSQPPRVREQRPRERPGFPPRGPRPGRGDMEQNDSDNRRIIRYPDSHQLFVGNLPH
          QEPPKPRVEAK.EVQSQPP.V.E..PR.RP.FP.RGPRPGRGD.E..D.DNRRII.YPDSHQLF.GNL.H
Retrocopy QEPPKPRVEAKTEVQSQPPPVCEE*PRQRPAFPARGPRPGRGDTELSDYDNRRIIHYPDSHQLFLGNLLH

Parental  DIDENELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILIAKPIMFRGEV-RLNVEEKKT
          DIDENEL..FFMSFGNVVEL.INTKGVG.KLPNFGFVVFDDSEPVQRILI.K.IMF.GEV..LNV..KKT
Retrocopy DIDENELE*FFMSFGNVVELHINTKGVGEKLPNFGFVVFDDSEPVQRILIVKLIMF*GEV<NLNVKKKKT

Parental  RAARERETRGGGDD-RRDIRRNDRGPGGPRGIVGGGMMRDRDGRGPPP
          RA.RE.ETRGG.DD..R.IRRND.GPGGPRGIVGG.MM....GRGPPP
Retrocopy RATREQETRGGSDD>GRVIRRNDQGPGGPRGIVGGRMMHEHNGRGPPP

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	0.09 RPM	66.87 RPM
SRP051959_heart	0.05 RPM	43.85 RPM
SRP051959_kidney	0.00 RPM	65.58 RPM
SRP051959_liver	0.02 RPM	37.54 RPM
SRP051959_lung	0.03 RPM	59.28 RPM
SRP051959_lymph_node	0.07 RPM	63.24 RPM
SRP051959_skeletal_muscle	0.02 RPM	51.17 RPM
SRP051959_spleen	0.11 RPM	65.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4164 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4164 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019897	1 retrocopy	retro_cjac_4164 ,
Echinops telfairi	ENSETEG00000016219	1 retrocopy	retro_etel_86,
Gorilla gorilla	ENSGGOG00000014947	1 retrocopy	retro_ggor_1763,
Otolemur garnettii	ENSOGAG00000000157	1 retrocopy	retro_ogar_810,
Ictidomys tridecemlineatus	ENSSTOG00000012975	1 retrocopy	retro_itri_1853,