RetrogeneDB ID:

retro_cjac_2259

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:111247964..111248817(-)
Located in intron of:ENSCJAG00000005110
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPZA1
Ensembl ID:ENSCJAG00000013548
Aliases:None
Description:capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]


Retrocopy-Parental alignment summary:






>retro_cjac_2259
ATGGCCAACTTCAATGATTGTGTGTCAGATGAGAAGGTACCCATAGCTGTTAAGTTCGTCACTCATGCACCCCAGGGGAA
TTTAATGAACTATTTAATGATGTTTGGCTACTACTTAATAATGACAATCTCCTCAGGGAAGGGGCAGCACATGCATTTTC
CCAGTATAACATGGATCGGTTCATGTCTGTGAAGATAGAAGGATATGAAGATCAGGTTTTAATTACAGGGCATGGTGACC
TAGGTAACAGCAGATTTTTAGATCCAAGAAACAAAATTTCCTTTAAATTTGATCACCTAGGAAAGAAGCAAGTGACCCCC
ACCCAGAAGAAGCTGATGGAGGTCTTAAGTCTTGGAGAGAATCTTGTGACTGTGCTTTACCAGCCTATGTGAAAGACCAT
TATTCCAGCGGCTTCTGTACTGTTTATGCGAAAACTATCCATGGGCAACAGACTATTATTGCATGTATTGAAAGCCACCA
GTTACAGCCTAAAAACTTCTGGAATGGTAGTTGGAGATCAGAGCAGAAGTTCACCATCACACTACCTACAGCCCAGGTGG
TTGGAGTGCTTAAGACTCAGGTTCACTATTATGAAGATGGCAATGTTCAGTTGGCTAGTCATAAAGATGTACAGGATTGA
CTAACTGTTTTGAATGAAGCCCAAACTGCCAAGGAGTTTATTAATATCACAGAGAATGCAGAAAATGAGTATCAGACAGC
AATTAGTAAAAACTATCAAACAATGCCAGATACCACATTTAAGGCATTGCGCAGGCAGCTTCCATTTACCCACACCAAAA
TCAACTGGAACAAGATAGTCAGCTACAAGATTGGCAAAGAAATGCAGAATGCT

ORF - retro_cjac_2259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMADFDDRVSDEEKVRIAAKFITHAP-PGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEG
MA.F.D.VSDE.KV.IA.KF.THAP.PGEFNE.FNDV.LLLNNDNLLREGAAHAF.QYNMD.F..VKIEG
RetrocopyMANFNDCVSDE-KVPIAVKFVTHAP<PGEFNELFNDVWLLLNNDNLLREGAAHAFSQYNMDRFMSVKIEG
ParentalYEDQVLITEHGDLGNSRFLDPRNKISFKFDHL-RKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSN
YEDQVLIT.HGDLGNSRFLDPRNKISFKFDHL.RKEASDP.PEE.DGGLKSWRESCD.AL.AYVKDHYS.
RetrocopyYEDQVLITGHGDLGNSRFLDPRNKISFKFDHL<RKEASDPHPEEADGGLKSWRESCDCALPAYVKDHYSS
ParentalGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVS
GFCTVYAKTI.GQQTIIACIESHQ.QPKNFWNG.WRSE.KFTIT.PTAQVVGVLK.QVHYYEDGNVQL.S
RetrocopyGFCTVYAKTIHGQQTIIACIESHQLQPKNFWNGSWRSEQKFTITLPTAQVVGVLKTQVHYYEDGNVQLAS
ParentalHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYK
HKDVQD.LTV.NEAQTAKEFI.I.ENAENEYQTAIS.NYQTM.DTTFKALRRQLP.T.TKI.WNKI.SYK
RetrocopyHKDVQD*LTVLNEAQTAKEFINITENAENEYQTAISKNYQTMPDTTFKALRRQLPFTHTKINWNKIVSYK
ParentalIGKEMQNA
IGKEMQNA
RetrocopyIGKEMQNA

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 1 .15 RPM 60 .86 RPM
SRP051959_heart 0 .61 RPM 25 .77 RPM
SRP051959_kidney 0 .78 RPM 43 .09 RPM
SRP051959_liver 0 .48 RPM 41 .44 RPM
SRP051959_lung 1 .06 RPM 66 .75 RPM
SRP051959_lymph_node 1 .14 RPM 114 .84 RPM
SRP051959_skeletal_muscle 0 .20 RPM 16 .33 RPM
SRP051959_spleen 0 .90 RPM 92 .50 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_2259 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2259 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2259 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000035701 retrocopy
retro_amel_219,
Callithrix jacchus ENSCJAG00000013548 3 retrocopies
retro_cjac_2259 , retro_cjac_2850, retro_cjac_4125,
Cavia porcellus ENSCPOG000000145321 retrocopy
retro_cpor_1155,
Dipodomys ordii ENSDORG000000006713 retrocopies
retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus ENSFCAG000000133032 retrocopies
retro_fcat_700, retro_fcat_746,
Homo sapiens ENSG000001164892 retrocopies
retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla ENSGGOG000000236771 retrocopy
retro_ggor_1216,
Latimeria chalumnae ENSLACG000000179631 retrocopy
retro_lcha_20,
Macaca mulatta ENSMMUG000000156682 retrocopies
retro_mmul_2612, retro_mmul_942,
Mus musculus ENSMUSG000000703724 retrocopies
retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys ENSNLEG000000041911 retrocopy
retro_nleu_1689,
Oryctolagus cuniculus ENSOCUG000000002706 retrocopies
retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii ENSOGAG000000140744 retrocopies
retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii ENSPPYG000000010212 retrocopies
retro_pabe_2116, retro_pabe_3789,
Pan troglodytes ENSPTRG000000011102 retrocopies
retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus ENSRNOG000000135381 retrocopy
retro_rnor_77,
Tupaia belangeri ENSTBEG000000017275 retrocopies
retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,


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