RetrogeneDB ID:

retro_cjac_127

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:31145152..31146400(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000016238
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSCJAG00000009931
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_127
ATGATGCTGGGCCCTGAGGGAGGTGAGGGCTTTGTGGTCAAGCTCCGTGGCCTTCCCTGGTCCTGCTCTGTTGAGGACGT
GCAGAACTTCCTCTCTGACTGCACGATTCACGATGGGGCCGCAGGTGTCCATTTCATCTACACTAGAGAGGGCAGGCAGA
GTGGTGAGGCTTTTGTTGAACTTGGATCAGAAGATGATGTAAAACTGGCTTTGAAAAAAGACAGGGAAAGCATGGGCCAC
CGGTACATAGAGGTGTTCAAGTCCCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGTGGTCCCAACAGTGCCGACAG
CGCCAATGATGGCTTCGTGCGGCTTCGAGGACTCCCATTTGGATGCACAAAGGAAGAAATTGTTCAGTTCTTCTCAGGGT
TGGAAATCGTGCCAAACGGGATCACATTGCCTGTGGACCCCGAGGGCAAGATTACAGGGGAAGCATTTGTGCAGTTTGCC
TCCCAGGAGTTAGCTGAGAAAGCTCTAGGGAAGCACAAGGAGAGGATAGGGCACAGGTACATCGAGGTGTTTAAGAGCAG
CCAGGAGGAAGTTAGGTCATACTCAGATCCCCCTCTGAAGTTCATGTCCGTGCAGCGGCCGGGGCCCTATGACCGCCCCG
GAACCGCCAGGAGGTATATTGGCATTGTGAAGCAGGCAGGCCTGGAGAGGATGCGGCCTGGTGCCTACAGCGCAGGCTAT
GGGGGCTATGAGGAGTACAGTGGCCTCAGCGATGGTTATGGCTTCACCACCGATCTGTTCGGGAGAGACCTCAGCTACTG
TCTCTCTGGAATGTATGACCACAGATACGGCGACAGTGAGTTCACAGTGCAGAGCACCACAGGCCACTGTGTCCACATGA
GGGGTCTGCCATACAAAGCGACAGAGAACGACATTTACAACTTCTTTTCTCCTCTCAATCCTGTGAGAGTCCATATTGAG
ATCGGCCCAGATGGAAGAGTGACGGGCGAAGCAGATGTTGAGTTTGCTACTCATGAAGAAGCTGTTGCAGCCATGTCCAA
AGACAGGGCTAACATGCAACACAGATACATAGAACTCTTCTTGAATTCGACAACAGGGGCCAGCAATGGGGCATATAGCA
GCCAGGTGATGCAAGGCATGGGGGTGTCTGCTGCCCAGGCCACTTATAGTGGCCTGGAGAGCCAGTCAGTGAGCGGCTGT
TATGGGGCCGGCTACAGTGGGCAGAACAGCATGGGTGGATATGACTAG

ORF - retro_cjac_127 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.06 %
Parental protein coverage: 91.31 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
MMLG.EGGEGFVVK.RGLPWSCS...VQ.F.SDC.I..GA.G..FIYTREGR.SGEAFVEL.SED.VKLA
RetrocopyMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKLA
ParentalLKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
LKKDRE.MGHRY.EVFKS...EMDWVLKH.GPNS.D.ANDGFVRLRGLPFGC.KEEIVQFFSGLEIVPNG
RetrocopyLKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNG
ParentalITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
ITLPVD..G..TGEAFVQFASQE.AEKAL.KHKERIGHRYIE.FKSS..EVR...DPP.K.M..QRPGPY
RetrocopyITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEVRSYSDPPLKFMSVQRPGPY
ParentalDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
DRPG..R.Y..I...AG.ERMR.GAY..GYGGY..Y.G..DGYGF..D.FGRDL.YC.SGM.DHRYGD..
RetrocopyDRPGTARRYIGIVKQAGLERMRPGAYSAGYGGYEEYSGLSDGYGFTTDLFGRDLSYCLSGMYDHRYGDSE
ParentalSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
.T.QSTTGHCVHMRGLPY.ATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHE.AVAAMSKD.A
RetrocopyFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRA
ParentalNMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGG---MGLSNQSSYGG
NMQHRY.ELFLNST.GAS.GAY..........S.A.A......SQ...G....G.S.Q.S.GG
RetrocopyNMQHRYIELFLNSTTGASNGAYSSQVMQGMGVSAAQATYSGLESQSVSGCYGAGYSGQNSMGG

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 70 .71 RPM 104 .97 RPM
SRP051959_heart 39 .54 RPM 135 .69 RPM
SRP051959_kidney 70 .80 RPM 164 .13 RPM
SRP051959_liver 73 .28 RPM 148 .38 RPM
SRP051959_lung 79 .69 RPM 207 .54 RPM
SRP051959_lymph_node 87 .67 RPM 285 .70 RPM
SRP051959_skeletal_muscle 39 .61 RPM 116 .09 RPM
SRP051959_spleen 71 .76 RPM 220 .23 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_127 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_127 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_127 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 30 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088882 retrocopies
retro_amel_57, retro_amel_9,
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Canis familiaris ENSCAFG000000003362 retrocopies
retro_cfam_200, retro_cfam_230,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG00000009931 1 retrocopy
retro_cjac_127 ,
Callithrix jacchus ENSCJAG000000191542 retrocopies
retro_cjac_292, retro_cjac_578,
Cavia porcellus ENSCPOG000000014855 retrocopies
retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Dipodomys ordii ENSDORG000000054531 retrocopy
retro_dord_3,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Felis catus ENSFCAG000000012042 retrocopies
retro_fcat_131, retro_fcat_27,
Homo sapiens ENSG000001690452 retrocopies
retro_hsap_3322, retro_hsap_4911,
Gorilla gorilla ENSGGOG000000258442 retrocopies
retro_ggor_1299, retro_ggor_177,
Myotis lucifugus ENSMLUG000000166251 retrocopy
retro_mluc_124,
Macaca mulatta ENSMMUG000000108431 retrocopy
retro_mmul_2,
Monodelphis domestica ENSMODG000000094363 retrocopies
retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Mustela putorius furoENSMPUG000000006931 retrocopy
retro_mputfur_156,
Mus musculus ENSMUSG000000078501 retrocopy
retro_mmus_142,
Nomascus leucogenys ENSNLEG000000266583 retrocopies
retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Otolemur garnettii ENSOGAG000000126312 retrocopies
retro_ogar_208, retro_ogar_498,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pongo abelii ENSPPYG000000161211 retrocopy
retro_pabe_110,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Rattus norvegicus ENSRNOG000000033991 retrocopy
retro_rnor_340,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Sus scrofa ENSSSCG000000140221 retrocopy
retro_sscr_70,
Ictidomys tridecemlineatus ENSSTOG000000163762 retrocopies
retro_itri_66, retro_itri_78,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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