RetrogeneDB ID:

retro_cjac_3528

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01183108.1:8691..9204(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000004059
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ZCCHC9
Ensembl ID:ENSCJAG00000019486
Aliases:None
Description:zinc finger, CCHC domain containing 9 [Source:HGNC Symbol;Acc:25424]


Retrocopy-Parental alignment summary:






>retro_cjac_3528
GAAGTAAGGGAAGAAATTGCAGTTGCTTTAAAGAAAGACAGTCAATGGGAAGGAAGAAGATTAAAAAGACAAGTGGCAAA
GAAAAATGCAGTGGTGTTTCTATTGTAGAAAACCTGGTCATGGAATTGCAGATTGCCCTGCACCCTTGAAAATCAACATA
CTGGAGTATGTTACAGGTGTGGGTCCACAGAGCACGAAATAACCAAGTGTAAGGCTAAAGTAGATCCGGCTCTTGGTGAA
TTTCCTTTCACAAAATGTTTTGTTTGTGGAGAAATGGGGCACCTCTCTAGAGCTTGTCCTGATAATCCCAAAGGACTCTA
TGCTGATGGTGGTGGTTGCAAACTTTGTGGCTCTGTGAAACATTTAAAGAAAGATTGCCTGGAAAATCAGAATTCAGATC
GAATGGTCACAGTTGGTCACTGGGCAAAGGGAATGAGTACAGATTATGAAGAAATTTTGGATGCACCTAAACCACAAAAA
CCCAAAACAAAAATACCTAAAGTTGTTAATTTT

ORF - retro_cjac_3528 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.75 %
Parental protein coverage: 64.21 %
Number of stop codons detected: 0
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalEVREEIAVALKKDSRREGRRL-KRQAAKKNA-MVCFHCRKPGHGIADCPA-ALENQDMGTGICYRCGSTE
EVREEIAVALKKDS..EGRRL.K....K......CF.CRKPGHGIADCPA..LENQ...TG.CYRCGSTE
RetrocopyEVREEIAVALKKDSQWEGRRL<KKTSGKEKC<QWCFYCRKPGHGIADCPA<TLENQH--TGVCYRCGSTE
ParentalHEITKCKAKVDPALGEFPFAKCFVCGEMGHLSRACPDNPKGLYADGGGCKLCGSVEHLKKDCPENQNSDR
HEITKCKAKVDPALGEFPF.KCFVCGEMGHLSRACPDNPKGLYADGGGCKLCGSV.HLKKDC.ENQNSDR
RetrocopyHEITKCKAKVDPALGEFPFTKCFVCGEMGHLSRACPDNPKGLYADGGGCKLCGSVKHLKKDCLENQNSDR
ParentalMVTVGRWVKGMSADYEEILDAPKLQKPKTKIPKVVNF
MVTVG.W.KGMS.DYEEILDAPK.QKPKTKIPKVVNF
RetrocopyMVTVGHWAKGMSTDYEEILDAPKPQKPKTKIPKVVNF

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 .80 RPM 5 .57 RPM
SRP051959_heart 0 .82 RPM 10 .59 RPM
SRP051959_kidney 0 .51 RPM 7 .94 RPM
SRP051959_liver 0 .35 RPM 7 .52 RPM
SRP051959_lung 0 .88 RPM 8 .20 RPM
SRP051959_lymph_node 1 .32 RPM 8 .13 RPM
SRP051959_skeletal_muscle 0 .79 RPM 9 .15 RPM
SRP051959_spleen 1 .03 RPM 9 .16 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_3528 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3528 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3528 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052651 retrocopy
retro_btau_1095,
Canis familiaris ENSCAFG000000087032 retrocopies
retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni ENSCHOG000000052683 retrocopies
retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus ENSCJAG00000019486 4 retrocopies
retro_cjac_1236, retro_cjac_2906, retro_cjac_3528 , retro_cjac_909,
Echinops telfairi ENSETEG000000038382 retrocopies
retro_etel_325, retro_etel_880,
Homo sapiens ENSG000001317321 retrocopy
retro_hsap_1799,
Gorilla gorilla ENSGGOG000000137901 retrocopy
retro_ggor_706,
Myotis lucifugus ENSMLUG000000018861 retrocopy
retro_mluc_799,
Macaca mulatta ENSMMUG000000206551 retrocopy
retro_mmul_797,
Mus musculus ENSMUSG000000216211 retrocopy
retro_mmus_1920,
Otolemur garnettii ENSOGAG000000025436 retrocopies
retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii ENSPPYG000000156041 retrocopy
retro_pabe_1476,
Pan troglodytes ENSPTRG000000170472 retrocopies
retro_ptro_1205, retro_ptro_602,
Rattus norvegicus ENSRNOG000000149272 retrocopies
retro_rnor_1164, retro_rnor_2160,
Sorex araneus ENSSARG000000085802 retrocopies
retro_sara_216, retro_sara_78,
Sarcophilus harrisii ENSSHAG000000145041 retrocopy
retro_shar_734,
Ictidomys tridecemlineatus ENSSTOG000000014072 retrocopies
retro_itri_422, retro_itri_696,
Tursiops truncatus ENSTTRG000000137961 retrocopy
retro_ttru_819,


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