RetrogeneDB ID: retro_cjac_1297

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:75148070..75148771(-)
• Located in intron of: ENSCJAG00000003410

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSCJAG00000000793
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_cjac_1297
GCCGAATGACTTTTGGCAGCTCAGAACCCACTCTCCCATGCTGACCGTCCTCATCAGCTGTTTGCAGATGCACCTCCTCC
ACCCTCTGCCCCCAATCCTGTGGTATCATCACTGGGGCTGGGCTTCCTCCACCAGGCATGCCTCCTTCTGGCTCCTTCCC
TCCCCCAGTGCTGCCTCCTGGAGCCCTCCCACCTGGGATACCTCCAGCCATGCCCCACCACCTATGCCGCCTGGGGCTGC
AGGACACGGCCCCCCTTCGGCAGGAACCCCAGGGCAGGACATCCTGGTCATGGACACTCACATCCTCATCCATTCCCACC
AGGTGGGATGCCCCATCCAGGGATGACTCAGATGCAGCTGGCACATCATGGCCCTCATGGCTTGGGACATCCTCCATGCT
GGACCCCCAGGCTCTGGGGGGGCAGCCACCGCCCCGACCACCACCTGGAATGCCTCATCCTGGACCTCCTCCAATGGGCA
TGCCCCCCCGAGGGCCTCCATTCGGATCTCCCATGGGTCACCCAGGTCCTATGCCTCCACATGATATGCATGGACCTCCT
CCACTGATGCCCCCCCATGGATACACTGGCCCTCCATGACCCCCACCCTATGGCTACCAGCGGGGTCCTCTCCCTCCACC
CAGACCCACTCCCCGGCCACCAGTTCCTCCTCGAGGCCCGCTTCGGGGCCCTCTCCCTCAG

Alignment

ORF - retro_cjac_1297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.56 %
• Parental protein coverage: 55.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLG-SGLPPPGMPPPGSFPPPVPPPGALPPGIPP
          AE.LLAAQNPLS.ADRPHQLFADAPPPPSAPNPVVSSLG..GLPPPGMPP.GSFPPPV.PPGALPPGIPP
Retrocopy AE*LLAAQNPLSHADRPHQLFADAPPPPSAPNPVVSSLG<AGLPPPGMPPSGSFPPPVLPPGALPPGIPP

Parental  AMP-PPPMPPGAAGHGPPSAGTPG-AGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHP-HAGP
          AMP.PPPMPPGAAGHGPPSAGTPG.AGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHP.HAGP
Retrocopy AMP<PPPMPPGAAGHGPPSAGTPG<AGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHP>HAGP

Parental  PGS-GGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYG
          PGS.GGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPH.M.GPPPLMPPHGYTGPP.PPPYG
Retrocopy PGS>GGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPHDMHGPPPLMPPHGYTGPP*PPPYG

Parental  YQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
          YQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
Retrocopy YQRGPLPPPRPTPRPPVPPRGPLRGPLPQ

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	3.93 RPM
SRP051959_heart	0.26 RPM	3.07 RPM
SRP051959_kidney	0.02 RPM	4.13 RPM
SRP051959_liver	0.15 RPM	2.49 RPM
SRP051959_lung	0.20 RPM	5.08 RPM
SRP051959_lymph_node	0.09 RPM	5.14 RPM
SRP051959_skeletal_muscle	0.09 RPM	2.51 RPM
SRP051959_spleen	0.06 RPM	3.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1297 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1297 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297 , retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,