RetrogeneDB ID: retro_cjac_3066

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:41236911..41237556(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3A
• Ensembl ID: ENSCJAG00000019373
• Aliases: None
• Description: general transcription factor IIIA [Source:HGNC Symbol;Acc:4662]

Sequence

>retro_cjac_3066
AAAAAATCCCACACAAAATCCAACTGGAAGAAAAATTTTGCATGCAAACACGAAAATCTGCAAAAGTAATATGTATGCAA
TTTTGGAGGATGTACGAAGACCTCTAAGAAGCATCGACTGCTGAAAATCCATCAGTGACAGCATGAAAAGAAATCACTAT
TCCAGTGTAACCTTGAAGTATGTGGAAAACACTTTGCTTCACCAAGCAGGCTGAGAGGACAGGGGCAGGCTCACCAGAAA
AATATATGTCAAAAGGGTTGTTCTTTTGTGGTAGAAACATGGACAGGACTTCCAAAGCACATGAGAGAAATCCATAAAAA
GGAAATAACATACGATGTATGCCAGAAAATATTCAAATGTGAAGATTATCTCAAGTGACCTGTGAAAACTCATGCCTCAG
AAAGAGATGTATGTCAACATCCTGGAGAAGACTGCAGCAGAACTATATTTAATCTTCAGAACTGTCTTTTTTCTTTTCCT
AAGGAGAAGCACTCATTTATGTGTGAACATGCTGGCCATGGCAAAAGGTTGGCTATGAAACAAAGTCTTAAAAGGCATGC
TATTGTGTATGAGCTTGACATGAATAAAATGAAGCTCAAAGTAAAACAATCTCCTGAAAAATGAAATTTGGCTTCTCATC
TCAGT

Alignment

ORF - retro_cjac_3066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.72 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKFNTKSNLKKHFERKHENQQKQYVCHFEGCKKTFKKHQQLKIHQCQHTGEPLFKCTQEGCGKHFASPSK
          .K..TKSN.KK.F..KHEN.QK.YVC.F.GC.KT.KKH..LKIHQ.QH....LF.C..E.CGKHFASPS.
Retrocopy KKSHTKSNWKKNFACKHENLQK*YVCNFGGCTKTSKKHRLLKIHQ*QHEKKSLFQCNLEVCGKHFASPSR

Parental  LKRHAKAHEGYVCQKGCCFVAKTWTELLKHVRETHKEEILCEICQKTFKRKDYLKQHMKTHAPERDVCRC
          L.....AH....CQKGC.FV..TWT.L.KH.RE.HK.EI....CQK.FK..DYLK...KTHA.ERDVC..
Retrocopy LRGQGQAHQKNICQKGCSFVVETWTGLPKHMREIHKKEITYDVCQKIFKCEDYLK*PVKTHASERDVCQH

Parental  PREGCGRTYTTVFNLQSHILSFHEERRPFVCEHAGCGRTFAMKQSLTRHAVVHDPDKKKMNLKVKKAREK
          P.E.C.RT....FNLQ....SF..E...F.CEHAG.G...AMKQSL.RHA.V...D..KM.LKVK...EK
Retrocopy PGEDCSRT---IFNLQNCLFSFPKEKHSFMCEHAGHGKRLAMKQSLKRHAIVYELDMNKMKLKVKQSPEK

Parental  RSLASRLS
          ..LAS.LS
Retrocopy *NLASHLS

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	15.24 RPM
SRP051959_heart	0.00 RPM	8.45 RPM
SRP051959_kidney	0.00 RPM	21.17 RPM
SRP051959_liver	1.34 RPM	31.30 RPM
SRP051959_lung	0.00 RPM	10.59 RPM
SRP051959_lymph_node	0.00 RPM	15.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	17.27 RPM
SRP051959_spleen	0.00 RPM	14.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3066 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3066 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066 ,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,