RetrogeneDB ID:

retro_cjac_2263

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:112272565..112273768(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023152
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC1A
Ensembl ID:ENSCJAG00000015859
Aliases:None
Description:actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]


Retrocopy-Parental alignment summary:






>retro_cjac_2263
GCGTCAACTGCCCAGAGTCCGCGAATCCTCCGCTCCGAGCCTGTCTGGACTCTCCCGACCCCAGCTTTTTCTCCTTTGAA
AACACTAAGAATAATGTCACTGCATCAGTTTTTACTAGAGCCAATCACCTGTCATGCCTGTAACAAGGATCGTACCCAGA
TTGCCCTCAGTCCCAATAATCACGAAGTACACATCTATAAGAAGAACGGGAGCCAGTGGGTAAAAGCTCATGAACTCAGG
GAACACAATGGACACATCACAGGTATTGACTGGGCTCCCAAGAGCGACCGCATCGTCACTTGTGCGGCAGACCGAAATGC
CTATGTCTGGAGTCAGAAAGATGGTATCTGGAAGCCAACCCTCGTGATCCTGAGAATTAATCGTGCAGCTACTTTTGTGA
AGTGGTCCCCTCTAGAGAACAAATTTGCTGTGGGAAGTGGAGCACGACTCATTTCCGTTTGTTACTTTGAGTCTGAAAAT
GACTGGTGGGTGAGCAAGCACATTAAAAACCCGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATACCAACAACGTTTT
GCTGGCAGCAGGATCATGTGACTTCAAATGCAGAGTGTTTTCTGCGTACATTAAAGAAGTGGATGAAAAGCCAGCCAGCA
CGCCCTGGGGTAGCAAAATGCCTTTTGGGCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGCGGCTGGGTCCACGGG
GTCAACTTCTCTGCCAGTGGGAGCTGCCTGGCCTGGGTCAGCCACGACAGCACCGTGTCTGTTGCTGATGCCTCAAAAAG
TGTGCAGGTCTCAACTCTGAAGACTGAGTTCCTGCCACTCCTGAGCGTGTCATTTGTCTCGGAAAACAGTGTTGTGGCTG
CTGGCCATGACTGCTGCCCAATGCTCTTTAACTATGATGACCGTGGCTGCCCGACCTTCGTCTCTAAGTTAGACATTCCA
AAACAGAGCATCCAACGCAACATGTCTGCCATGGAACGCTTCCGCCACATGGACAAGAGGGCCACAACTGAGGACCGCAA
CACGGCCTTGGAAACGCTGCACCAGAATAGCATCACTCAAATCTCTATTTATGAGGTGGACAAGCAAGATTGTCGCAAAT
TTTGCACTACTGGCATCGATGGAGCCATGACAATTTGGGATTTCAAGACCCTCGAGTCTTTCATCCAGGGCCTCCAGATA
ATG

ORF - retro_cjac_2263 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.26 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalASTAQSPRILRSEPVWTPRTPAFSPLKTLRIMSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNG
ASTAQSPRILRSEPVWT..TPAFSPLKTLRIMSLHQFLLEPITCHA.N.DRTQIALSPNNHEVHIYKKNG
RetrocopyASTAQSPRILRSEPVWTLPTPAFSPLKTLRIMSLHQFLLEPITCHACNKDRTQIALSPNNHEVHIYKKNG
ParentalSQWVKAHELKEHNGHITGIDWAPKSDRIVTCGADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLEN
SQWVKAHEL.EHNGHITGIDWAPKSDRIVTC.ADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLEN
RetrocopySQWVKAHELREHNGHITGIDWAPKSDRIVTCAADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLEN
ParentalKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEK
KFAVGSGARLISVCYFESENDWWVSKHIK.PIRSTVLSLDWH.NNVLLAAGSCDFKCRVFSAYIKEVDEK
RetrocopyKFAVGSGARLISVCYFESENDWWVSKHIKNPIRSTVLSLDWHTNNVLLAAGSCDFKCRVFSAYIKEVDEK
ParentalPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPL
PASTPWGSKMPFGQLMSEFGGSGTGGWVHGV.FSASGS.LAWVSHDSTVSVADASKSVQVSTLKTEFLPL
RetrocopyPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVNFSASGSCLAWVSHDSTVSVADASKSVQVSTLKTEFLPL
ParentalLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDRNTAL
LSVSFVSENSVVAAGHDCCPMLFNYDDRGC.TFVSKLDIPKQSIQRNMSAMERFR.MDKRATTEDRNTAL
RetrocopyLSVSFVSENSVVAAGHDCCPMLFNYDDRGCPTFVSKLDIPKQSIQRNMSAMERFRHMDKRATTEDRNTAL
ParentalETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
ETLHQNSITQ.SIYEVDKQDCRKFCTTGIDGAMTIWDFKTLES.IQGL.IM
RetrocopyETLHQNSITQISIYEVDKQDCRKFCTTGIDGAMTIWDFKTLESFIQGLQIM

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 48 .35 RPM
SRP051959_heart 0 .09 RPM 22 .91 RPM
SRP051959_kidney 0 .07 RPM 25 .87 RPM
SRP051959_liver 0 .06 RPM 28 .98 RPM
SRP051959_lung 0 .11 RPM 33 .19 RPM
SRP051959_lymph_node 0 .11 RPM 20 .11 RPM
SRP051959_skeletal_muscle 0 .07 RPM 13 .69 RPM
SRP051959_spleen 0 .11 RPM 24 .94 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_2263 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2263 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2263 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063221 retrocopy
retro_amel_1431,
Bos taurus ENSBTAG000000042421 retrocopy
retro_btau_1486,
Callithrix jacchus ENSCJAG000000158491 retrocopy
retro_cjac_2365,
Callithrix jacchus ENSCJAG00000015859 3 retrocopies
retro_cjac_2141, retro_cjac_2165, retro_cjac_2263 ,
Cavia porcellus ENSCPOG000000017772 retrocopies
retro_cpor_452, retro_cpor_981,
Dipodomys ordii ENSDORG000000160591 retrocopy
retro_dord_593,
Equus caballus ENSECAG000000164671 retrocopy
retro_ecab_185,
Homo sapiens ENSG000002416852 retrocopies
retro_hsap_2010, retro_hsap_3191,
Loxodonta africana ENSLAFG000000140241 retrocopy
retro_lafr_1006,
Macropus eugenii ENSMEUG000000056098 retrocopies
retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus ENSMLUG000000109121 retrocopy
retro_mluc_1432,
Macaca mulatta ENSMMUG000000193422 retrocopies
retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica ENSMODG000000013039 retrocopies
retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus ENSMUSG000000296211 retrocopy
retro_mmus_1373,
Nomascus leucogenys ENSNLEG000000108522 retrocopies
retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus ENSOCUG000000039441 retrocopy
retro_ocun_1130,
Otolemur garnettii ENSOGAG000000108706 retrocopies
retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii ENSPPYG000000258164 retrocopies
retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes ENSPTRG000000338192 retrocopies
retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii ENSSHAG000000106732 retrocopies
retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus ENSSTOG000000016601 retrocopy
retro_itri_1834,
Tupaia belangeri ENSTBEG000000113813 retrocopies
retro_tbel_1237, retro_tbel_1241, retro_tbel_82,


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