RetrogeneDB ID:

retro_cjac_1157

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:13:61447422..61448650(-)
Located in intron of:ENSCJAG00000020629
Retrocopy
information
Ensembl ID:ENSCJAG00000020637
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP4
Ensembl ID:ENSCJAG00000001021
Aliases:None
Description:retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]


Retrocopy-Parental alignment summary:






>retro_cjac_1157
ATGGAAGAATGAGTGGTCAATGAGGAGTACAAAATTTGGAAAAAGAACACTCCTTTTCTTTGTGATGTGGTGACGACCCA
TGCTCTGGAGTGGCCTAGCCTAACTGCCCAGTGGCTTCTAGATGTAACCAGACCAGAAGGGAAAAGATTTCAGCATTCAT
TGACTTGTCCTGGGAACACAGACATTGGATGAACAAAACCATCTTGTTATAGTCAGAGTGCAACTTCCTAATGATGATGC
TCAGTTTGATGTGTCACACTACAACAGTGAGAAAGGGGAATTCAGAGGTTTTGGTTCAGTTAGTGGAAAACATGAAATAG
AAATCAAGATCAACCATGAAGGAGAAGTAAACAGGGCCCGTTACATGCCCCAGAACCCTTGTATCATTACAACAGACTCC
TTCCAGTGATGTTCTTGTCTTTGACTATACGAAACATCCTTCTAAACCAGATCCTTCTAGAGAATGCAACCCAGACTTGC
ATCTCCGTGGACATCAGAAGGAAGGCTATGAGCTTTCTTGGAACCCAAATCTCAGTGGGCACTTATGTAGTGCTTCAGAT
GACCACACCATCTGCCTGTGGGACATCAGTGCTGTTCCAAAGGAGGGAAAAGTGGTGGAGGCGAAGACCATCTTTACAGG
GCACACAGCAGTACATGTTTTCTGGCATCTGCTCCATGAGTCTCTGTTTGGATCAGTTGCTGATGATCAGAAACTTATAA
TTTGGGATACTCATTCAAACAATACTTCCAACCACTCCGTTGATGCTCACACTGCTGAAGTGAACTGCCTCTCTTTCAAT
CCTTATAGTGAGTTCATTCTTGCCAGAGGATCAGCTGACAAGACTTTGCCTTGTGGGATCTGAGAAATCTGAAACTTAAG
TTGCATTCCTTTGAATCACATAAGGATGAAATGTTCCAGATTCAGTGGTCACTTCACAATGAGACTATTTTGGCTTCCAG
TGGTACTGATTACAGACTGAATGTCTGGGATTTAATTAAAATTGGAGAGGAACAATCCCCAGAAGATGCAGAAGACGGGC
CACCAGAGTTGTTGTTTATTCGTGGTGGTCACACTGCCAAGATACCTGATTTCTCTTGGAATCCCAGTGACCCTTGGGTG
ATTTGTTCTGAATCAGAAGACAGTATCATGCAAGTGTGGCAAATGGCAGAGAACATTTATAATGATGAAGACCCTGAAGG
AAGCGTGGATCTGGAAGGACAAGGGTCC

ORF - retro_cjac_1157 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.01 %
Parental protein coverage: 97.41 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGK-DFSIHRLVLGTHTSDEQNHLV
.EE.V.NEEYKIWKKNTPFL.D.V.THALEWPSLTAQWL.DVTRPEGK.DFSIH.LVLGT.T.DEQNHLV
RetrocopyMEE*VVNEEYKIWKKNTPFLCDVVTTHALEWPSLTAQWLLDVTRPEGK>DFSIH*LVLGTQTLDEQNHLV
ParentalIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIAT-KTPSSDV
I..VQLPNDDAQFD.SHY.SEKGEF.GFGSVSGK.EIEIKINHEGEVNRARYMPQNPC.I.T..TPSSDV
RetrocopyIVRVQLPNDDAQFDVSHYNSEKGEFRGFGSVSGKHEIEIKINHEGEVNRARYMPQNPC-IIT>QTPSSDV
ParentalLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDA
LVFDYTKHPSKPDPS.ECNPDL.LRGHQKEGY.LSWNPNLSGHL.SASDDHTICLWDISAVPKEGKVV.A
RetrocopyLVFDYTKHPSKPDPSRECNPDLHLRGHQKEGYELSWNPNLSGHLCSASDDHTICLWDISAVPKEGKVVEA
ParentalKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFIL
KTIFTGHTAV...V.WHLLHESLFGSVADDQKL.IWDT.SNNTS...HSVDAHTAEVNCLSFNPYSEFIL
RetrocopyKTIFTGHTAV--HVFWHLLHESLFGSVADDQKLIIWDTHSNNTS--NHSVDAHTAEVNCLSFNPYSEFIL
ParentalATGSADKTV-ALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPED
A.GSADKT..ALWDLRNLKLKLHSFESHKDE.FQ.QWS.HNETILASSGTD.RLNVWDL.KIGEEQSPED
RetrocopyARGSADKTL<ALWDLRNLKLKLHSFESHKDEMFQIQWSLHNETILASSGTDYRLNVWDLIKIGEEQSPED
ParentalAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS
AEDGPPELLFI.GGHTAKI.DFSWNP..PWVICS.SED.IMQVWQMAENIYNDEDPEGSVD.EGQGS
RetrocopyAEDGPPELLFIRGGHTAKIPDFSWNPSDPWVICSESEDSIMQVWQMAENIYNDEDPEGSVDLEGQGS

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 .60 RPM 58 .49 RPM
SRP051959_heart 0 .32 RPM 50 .20 RPM
SRP051959_kidney 0 .35 RPM 78 .14 RPM
SRP051959_liver 0 .48 RPM 56 .36 RPM
SRP051959_lung 1 .56 RPM 67 .14 RPM
SRP051959_lymph_node 5 .11 RPM 75 .43 RPM
SRP051959_skeletal_muscle 0 .07 RPM 44 .11 RPM
SRP051959_spleen 1 .37 RPM 78 .66 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_1157 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1157 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1157 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 75 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG00000001021 7 retrocopies
retro_cjac_1157 , retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Gorilla gorilla ENSGGOG000000113134 retrocopies
retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Monodelphis domestica ENSMODG000000174156 retrocopies
retro_mdom_1542, retro_mdom_1833, retro_mdom_1873, retro_mdom_1900, retro_mdom_563, retro_mdom_765,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Otolemur garnettii ENSOGAG000000116322 retrocopies
retro_ogar_3079, retro_ogar_3297,
Procavia capensis ENSPCAG000000110301 retrocopy
retro_pcap_116,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,
Tupaia belangeri ENSTBEG000000022363 retrocopies
retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
Vicugna pacos ENSVPAG000000118764 retrocopies
retro_vpac_333, retro_vpac_419, retro_vpac_652, retro_vpac_94,


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