RetrogeneDB ID:

retro_cjac_3358

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01174550.1:34641..35837(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000005117
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT19
Ensembl ID:ENSCJAG00000029756
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3358
ATGACTTCCTACAGCTATCGCCAGTCGTCCACGTCGTCCTTCGGGGGCCTGGGCGGCGGCCCCGTGCGTTTTGGGCCGGG
TGTCGCCTTTCGCGCACCTAGCATACACTGGGGCTCCGGCGGCCGCGGCGTGTCCGTGTCCACCACTCGCTTCGTGTCCT
CGTCCTCCTCGGGGGGCTACGGCGGCGGCTATGGCGGCATCCTGGCCACTTCCGACGGGCTGCTGGCGGGCAACGAGAAG
CTCACCATGCAGAACCTCAACGACCGCCTGGCCTCCTACCTGGACAAGGTGCGCGCCCTGGAGGCGGCCAACGGCGAGCT
GGAGGTGAAGATCCGCGACTGGTACCAGAAGCAGGGGCCCGGGCCCTCCCGCGACTACAGCCACTACTACAAGACCAACC
AGGACCTGCGGGACCAGATTCTTGGTGCCACCATTGAGAACTCCAGGATTGTCCTGCAGATTGACAATGCCCGTCTGGCT
GCAGATGACTTCCGAACCAAGTTTGAGACGGAGCAGGCTTTGCGCGTGAGCGTGGAGGCCGACATCAACGGCTGCGCAAG
GTGCTGGATGAGCTGACCCTGGCCAGGACTGACCTGGAAATGCAGATTGAAGGGCTGAAGGAAGAGCTGGCCTACCTGAA
GAAGAACCATGAGGAGGAACTCAGTGTGCTGAGGGGCCAAGTGGGAGGCCAGGTCAGTGTGGAGGTGGATTCAGCTCCAG
GCACCGATCTCGCCAAGATCCTGAGTGACATGCGAAGCCAATATGAGGTCATGGCCGAGCAGAACCGGAAGGATGCTGAA
GCCTGGTTCACCAGCCGGACTGAAGAACTGAACCGGGAGGTCGCTGTCCACAGAGAGCAGCTCCAGATGAGCAACACCGA
GGTCAGTGACCTGCGGCGCACCCTCCAGGGTCTTGAGATTGAGCTGCAGTCACAGCTGAGCATGAAAGCCGGCTTGGAAG
GCACACTGGCAGAAACGGAGGCGCGCTTTGGAGCCCAGCTGGCGGAGATCCAGGCGCGGATCAGTGGTATTGAAGCCCAG
CTGGGCGATGTGCGGGCTGATAGTGAGCGGCAGAATCAGGAGTACCATCGGCTCTTGGACGTCAAGTCGCGGCTGGAGCA
GGAGATCGCCACCTACCGGAGCCTGCTGGAGGGCCGGGAAGATCGCTACAACAACCTGTCTGCCTCCAAGGTCCTC

ORF - retro_cjac_3358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.25 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMTSYSYRQSSTSSFGGLGGASVRFGPGVAFRAPSIHGGSGGRGVSVSSTRFVSSSSSGGYGGGYGGILAT
MTSYSYRQSSTSSFGGLGG..VRFGPGVAFRAPSIH.GSGGRGVSVS.TRFVSSSSSGGYGGGYGGILAT
RetrocopyMTSYSYRQSSTSSFGGLGGGPVRFGPGVAFRAPSIHWGSGGRGVSVSTTRFVSSSSSGGYGGGYGGILAT
ParentalSDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKIRDWYQKQGPGPSRDYSHYYKTIQDLRDQI
SDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKIRDWYQKQGPGPSRDYSHYYKT.QDLRDQI
RetrocopySDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKIRDWYQKQGPGPSRDYSHYYKTNQDLRDQI
ParentalLGATIENSRIVLQIDNARLAADDFRTKFETEQALRMSVEADING-LRRVLDELTLARTDLEMQIEGLKEE
LGATIENSRIVLQIDNARLAADDFRTKFETEQALR.SVEADING.LR.VLDELTLARTDLEMQIEGLKEE
RetrocopyLGATIENSRIVLQIDNARLAADDFRTKFETEQALRVSVEADING<LRKVLDELTLARTDLEMQIEGLKEE
ParentalLAYLKKNHEEELSVLRGQVGGQVSVEVDSAPGTDLAKILSDMRSQYEVMAEQNRKDAEAWFTSRSEELNR
LAYLKKNHEEELSVLRGQVGGQVSVEVDSAPGTDLAKILSDMRSQYEVMAEQNRKDAEAWFTSR.EELNR
RetrocopyLAYLKKNHEEELSVLRGQVGGQVSVEVDSAPGTDLAKILSDMRSQYEVMAEQNRKDAEAWFTSRTEELNR
ParentalEVAVHREQLQMSNTEVSDLRRTLQGLEIELQSQLSMKAGLESTLAETEARFGAQLAEIQARISGIEAQLG
EVAVHREQLQMSNTEVSDLRRTLQGLEIELQSQLSMKAGLE.TLAETEARFGAQLAEIQARISGIEAQLG
RetrocopyEVAVHREQLQMSNTEVSDLRRTLQGLEIELQSQLSMKAGLEGTLAETEARFGAQLAEIQARISGIEAQLG
ParentalDVRADSERQNQEYHRLLDVKSRLEQEIATYRSLLEGQEDRYNNLSASKVL
DVRADSERQNQEYHRLLDVKSRLEQEIATYRSLLEG.EDRYNNLSASKVL
RetrocopyDVRADSERQNQEYHRLLDVKSRLEQEIATYRSLLEGREDRYNNLSASKVL

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 .27 RPM 290 .23 RPM
SRP051959_heart 0 .00 RPM 4 .95 RPM
SRP051959_kidney 0 .00 RPM 2 .37 RPM
SRP051959_liver 0 .26 RPM 1 .75 RPM
SRP051959_lung 0 .11 RPM 44 .90 RPM
SRP051959_lymph_node 0 .00 RPM 0 .32 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .09 RPM
SRP051959_spleen 0 .00 RPM 1 .85 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_3358 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3358 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3358 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000029756 9 retrocopies
retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358 , retro_cjac_633,
Equus caballus ENSECAG000000140862 retrocopies
retro_ecab_76, retro_ecab_931,
Echinops telfairi ENSETEG000000078816 retrocopies
retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens ENSG000001713453 retrocopies
retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla ENSGGOG000000169013 retrocopies
retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii ENSMEUG000000161583 retrocopies
retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta ENSMMUG000000186534 retrocopies
retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys ENSNLEG000000107873 retrocopies
retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus ENSOCUG000000161321 retrocopy
retro_ocun_1884,
Otolemur garnettii ENSOGAG000000243061 retrocopy
retro_ogar_1301,
Ochotona princeps ENSOPRG000000079082 retrocopies
retro_opri_337, retro_opri_673,
Pongo abelii ENSPPYG000000084163 retrocopies
retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes ENSPTRG000000091683 retrocopies
retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus ENSSTOG000000144032 retrocopies
retro_itri_1514, retro_itri_697,


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