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


Retrocopy-Parental alignment summary:






>retro_cjac_1297
GCCGAATGACTTTTGGCAGCTCAGAACCCACTCTCCCATGCTGACCGTCCTCATCAGCTGTTTGCAGATGCACCTCCTCC
ACCCTCTGCCCCCAATCCTGTGGTATCATCACTGGGGCTGGGCTTCCTCCACCAGGCATGCCTCCTTCTGGCTCCTTCCC
TCCCCCAGTGCTGCCTCCTGGAGCCCTCCCACCTGGGATACCTCCAGCCATGCCCCACCACCTATGCCGCCTGGGGCTGC
AGGACACGGCCCCCCTTCGGCAGGAACCCCAGGGCAGGACATCCTGGTCATGGACACTCACATCCTCATCCATTCCCACC
AGGTGGGATGCCCCATCCAGGGATGACTCAGATGCAGCTGGCACATCATGGCCCTCATGGCTTGGGACATCCTCCATGCT
GGACCCCCAGGCTCTGGGGGGGCAGCCACCGCCCCGACCACCACCTGGAATGCCTCATCCTGGACCTCCTCCAATGGGCA
TGCCCCCCCGAGGGCCTCCATTCGGATCTCCCATGGGTCACCCAGGTCCTATGCCTCCACATGATATGCATGGACCTCCT
CCACTGATGCCCCCCCATGGATACACTGGCCCTCCATGACCCCCACCCTATGGCTACCAGCGGGGTCCTCTCCCTCCACC
CAGACCCACTCCCCGGCCACCAGTTCCTCCTCGAGGCCCGCTTCGGGGCCCTCTCCCTCAG

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:

ParentalAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLG-SGLPPPGMPPPGSFPPPVPPPGALPPGIPP
AE.LLAAQNPLS.ADRPHQLFADAPPPPSAPNPVVSSLG..GLPPPGMPP.GSFPPPV.PPGALPPGIPP
RetrocopyAE*LLAAQNPLSHADRPHQLFADAPPPPSAPNPVVSSLG<AGLPPPGMPPSGSFPPPVLPPGALPPGIPP
ParentalAMP-PPPMPPGAAGHGPPSAGTPG-AGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHP-HAGP
AMP.PPPMPPGAAGHGPPSAGTPG.AGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHP.HAGP
RetrocopyAMP<PPPMPPGAAGHGPPSAGTPG<AGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHP>HAGP
ParentalPGS-GGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYG
PGS.GGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPH.M.GPPPLMPPHGYTGPP.PPPYG
RetrocopyPGS>GGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPHDMHGPPPLMPPHGYTGPP*PPPYG
ParentalYQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
YQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
RetrocopyYQRGPLPPPRPTPRPPVPPRGPLRGPLPQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_1297 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1297 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1297 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000124952 retrocopies
retro_btau_1385, retro_btau_592,
Canis familiaris ENSCAFG000000116173 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 ENSCPOG000000082671 retrocopy
retro_cpor_234,
Echinops telfairi ENSETEG000000089631 retrocopy
retro_etel_1310,
Homo sapiens ENSG000001433681 retrocopy
retro_hsap_1356,
Gorilla gorilla ENSGGOG000000047611 retrocopy
retro_ggor_1056,
Macaca mulatta ENSMMUG000000072561 retrocopy
retro_mmul_2191,
Mustela putorius furoENSMPUG000000055632 retrocopies
retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus ENSOCUG000000046141 retrocopy
retro_ocun_1239,
Pongo abelii ENSPPYG000000009121 retrocopy
retro_pabe_1124,
Pan troglodytes ENSPTRG000000012431 retrocopy
retro_ptro_930,
Pteropus vampyrus ENSPVAG000000141711 retrocopy
retro_pvam_931,
Rattus norvegicus ENSRNOG000000211811 retrocopy
retro_rnor_2350,
Ictidomys tridecemlineatus ENSSTOG000000006842 retrocopies
retro_itri_1153, retro_itri_487,


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