RetrogeneDB ID:

retro_cjac_2280

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:137157358..137158321(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000018072
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000002214
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2280
ATGGTGCCGAAGCCAGACCCGAAGCCTAAATTCCAGGAGGGTGAGCGAGTGCGGTGCTTTCATGGGCCTCTTCTGTATGA
AGCAAAGTGTGTAAAGGTTGCCTTAAAGGACAAACAAGTGAAATACTTCATACATTACAGTGGTTGAATAAAAATTGGGA
TGAGTGGGTTCCGGAGAGCCAGGTACTCAAATATGTGGACACCAATTTGCAGAAACAGCGAGAACTTCAAAAAGCCAATC
AGGAGCAGTATGCAGAGGGGAAGATGAGAGGGGCTGCCCCAGGAAAGAAGACGTCTGGTCTGCAACAGAAAAATGTTGAA
GTGAAAACAAAAAAGAACAAACAGAAAACACCGGGACATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTCG
GAAAAGGGCCCGGGTAGATCCTACTGTTGAAAATGAAACATTCATGAACAGAGTTGAAGTTAAAGTAAAGATTCCTGAAG
AACTAAAATCATGGCTTGTTGATGACTGGGACTTAATTACCAGGCAAAAGCAGCTCTTTTATCTTCCTCTCAGGAAGAAT
GTAGATTCCATTCTTGAGGATTATGCAAATGACAATAAATCTCGTGGAAACACAGATAATAAGGAGTATGCGGTTAATGA
AGTTGTGGCAGGGACAAAAGAATACTTCAATGTAATGTTGGGTACCCAGCTACTCTACAAATTTGAGAGAACACAGTATG
CTGAAATTCTTGCAGATCACCCTGATGCATCCATGTCCCAGGCGTTATGGGGCGCCACATCTACTGAGGCTATTTGTACG
AATTGGAGCAATGTTGGCCTATACACCTCTGGATGAGAAGAGCCTTGCTTTATTACTGAATTATCTTCACGATTTCCTAA
AGTACGTAGCAAAGAAGTCAGCAACTTTATTTAGTGCCCGTGATTATGAAGTGGCTCCTCCTGAGTACCATCGGAAAGCT
GTG

ORF - retro_cjac_2280 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.92 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSG-WNKNWDEWVPESRVLKYVDTN
M.PK.DPKPKFQEGERV.CFHGPLLYEAKCVKVA.KDKQVKYFIHYSG..NKNWDEWVPES.VLKYVDTN
RetrocopyMVPKPDPKPKFQEGERVRCFHGPLLYEAKCVKVALKDKQVKYFIHYSG<LNKNWDEWVPESQVLKYVDTN
ParentalLQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRAR
LQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPG.GDGGSTSETPQPPRK.RAR
RetrocopyLQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGHGDGGSTSETPQPPRK-RAR
ParentalVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDN
VDPTVENE.TFMNRVEVKVKIPEELK.WLVDDWDLITRQKQLFYLP..KNVDSILEDYAN..KSRGNTDN
RetrocopyVDPTVENE-TFMNRVEVKVKIPEELKSWLVDDWDLITRQKQLFYLPLRKNVDSILEDYANDNKSRGNTDN
ParentalKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQV-YGAPHLLRLFVRIGAMLAYTP
KEYAVNEVVAG.KEYFNVMLGTQLLYKFER.QYAEILADHPDA.MSQ..YGAPHLLRLFVRIGAMLAYTP
RetrocopyKEYAVNEVVAGTKEYFNVMLGTQLLYKFERTQYAEILADHPDASMSQA>YGAPHLLRLFVRIGAMLAYTP
ParentalLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
LDEKSLALLLNYLHDFLKY.AK.SATLFSA.DYEVAPPEYHRKAV
RetrocopyLDEKSLALLLNYLHDFLKYVAKKSATLFSARDYEVAPPEYHRKAV

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 .20 RPM 41 .34 RPM
SRP051959_heart 0 .28 RPM 63 .99 RPM
SRP051959_kidney 0 .60 RPM 72 .19 RPM
SRP051959_liver 0 .28 RPM 40 .90 RPM
SRP051959_lung 0 .16 RPM 58 .89 RPM
SRP051959_lymph_node 0 .25 RPM 43 .58 RPM
SRP051959_skeletal_muscle 0 .44 RPM 34 .22 RPM
SRP051959_spleen 0 .34 RPM 52 .25 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_2280 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2280 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2280 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123441 retrocopy
retro_amel_124,
Bos taurus ENSBTAG000000109881 retrocopy
retro_btau_137,
Canis familiaris ENSCAFG000000141131 retrocopy
retro_cfam_20,
Callithrix jacchus ENSCJAG00000002214 5 retrocopies
retro_cjac_2113, retro_cjac_2280 , retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Cavia porcellus ENSCPOG000000037783 retrocopies
retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus ENSECAG000000080911 retrocopy
retro_ecab_62,
Felis catus ENSFCAG000000121971 retrocopy
retro_fcat_75,
Homo sapiens ENSG000001857873 retrocopies
retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla ENSGGOG000000168263 retrocopies
retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana ENSLAFG000000098511 retrocopy
retro_lafr_62,
Myotis lucifugus ENSMLUG000000017561 retrocopy
retro_mluc_324,
Macaca mulatta ENSMMUG000000229261 retrocopy
retro_mmul_1064,
Monodelphis domestica ENSMODG000000115172 retrocopies
retro_mdom_150, retro_mdom_158,
Mustela putorius furoENSMPUG000000154291 retrocopy
retro_mputfur_180,
Mus musculus ENSMUSG000000622709 retrocopies
retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys ENSNLEG000000086783 retrocopies
retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus ENSOCUG000000151172 retrocopies
retro_ocun_108, retro_ocun_21,
Otolemur garnettii ENSOGAG000000060474 retrocopies
retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii ENSPPYG000000067034 retrocopies
retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes ENSPTRG000000073513 retrocopies
retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus ENSRNOG000000144106 retrocopies
retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sorex araneus ENSSARG000000045191 retrocopy
retro_sara_15,
Sarcophilus harrisii ENSSHAG000000184021 retrocopy
retro_shar_393,
Sus scrofa ENSSSCG000000017691 retrocopy
retro_sscr_93,
Ictidomys tridecemlineatus ENSSTOG000000132943 retrocopies
retro_itri_111, retro_itri_1545, retro_itri_1608,
Tupaia belangeri ENSTBEG000000018978 retrocopies
retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus ENSTTRG000000166061 retrocopy
retro_ttru_472,
Vicugna pacos ENSVPAG000000088471 retrocopy
retro_vpac_229,


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