RetrogeneDB ID:

retro_ptro_1248

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:18:3392086..3392797(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MRTO4
Ensembl ID:ENSPTRG00000000262
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1248
ATGCCCAAATCCAAGCATGACAGGAAGTCCCTAATCAAAACTGCCAAGAAAGGCTTGGAATTGAAACAACACCTGATAGA
AGAGCTTCGGAAACGTGTGGACACTGATAAGTACCTTTCCATCTCTCTGTGGCCAACACGTGGAACAGCAAGCTGAAGGA
CATCCGGAATGCCTGGAAGCACAGCCGGATGTTCTTTGGCAAAAACAAGGTGATGATGGCGGCCTTGGGTCGGAGCCCAT
TGGGTGAGTGCAAAGACAACCTGCACCAGGTCAGCAAAACGTTGAGGGGTGAAGCGGATCTCCTGTTCACCAACCACAGG
AAGGAGGAGGTGAATGAGTGGTTCACAGAATACACGGAAATGGACTACAGCTGAGCTGTAACAAAGCAGCTTTCACCGTG
AGCCTGGACCCAGGGCCCCTGGAGCAGTTCCCCACCCCATGAAGCCACAGCTGAGGCAGCCGGGCCTGCCCACCACCTTT
GAGAGAGGTGTGGCGAGCCTGCTGTCCGCCAATGAGGTGTGCAAGGAGGGCCACCTGCTGGCCCCGGAGCAGGCTGGTGT
TCTGATGCTTTCTGGGTATGAGATGGCTGAATTTAAGGTGACCATCAAATACATGTGGGATGTACAGTCGGGAAGGGTCC
AGCAGATGGGAGACGACCTGCCAGAAAGCGCGTCCAACTCAGCAGAAGAATCAGACTCAGACGATGATGAC

ORF - retro_ptro_1248 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.17 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYL-FIFSVANMRNSKLKDIRNAWKHSRMFFGK
MPKSK.D.K.SL.KTAKKGLELKQ.LIEELRK.VDT.KYL.F..SVAN..NSKLKDIRNAWKHSRMFFGK
RetrocopyMPKSKHDRK-SLIKTAKKGLELKQHLIEELRKRVDTDKYL<FHLSVANTWNSKLKDIRNAWKHSRMFFGK
ParentalNKVMMVALGRSPSDEYKDNLHQVSKRLRGEVGLLFTNRTKEEVNEWFTKYTEMDYARAG-NKAAFTVSLD
NKVMM.ALGRSP..E.KDNLHQVSK.LRGE..LLFTN..KEEVNEWFT.YTEMDY..A..NKAAFTVSLD
RetrocopyNKVMMAALGRSPLGECKDNLHQVSKTLRGEADLLFTNHRKEEVNEWFTEYTEMDYS*AV<NKAAFTVSLD
ParentalPGPLEQFP-HSMEPQLRQLGLPTALKRGVVTLLSDYEVCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYM
PGPLEQFP.H.M.PQLRQ.GLPT...RGV..LLS..EVCKEG..L.PEQA.VL.L.GYEMAEFKVTIKYM
RetrocopyPGPLEQFP<HPMKPQLRQPGLPTTFERGVASLLSANEVCKEGHLLAPEQAGVLMLSGYEMAEFKVTIKYM
ParentalWDSQSGRFQQMGDDLPESASESTEESDSEDDD
WD.QSGR.QQMGDDLPESAS.S.EESDS.DDD
RetrocopyWDVQSGRVQQMGDDLPESASNSAEESDSDDDD

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
SRP007412_brain_prefrontal_cortex 0 .04 RPM 44 .27 RPM
SRP007412_cerebellum 0 .04 RPM 24 .63 RPM
SRP007412_heart 0 .03 RPM 11 .80 RPM
SRP007412_kidney 0 .00 RPM 24 .24 RPM
SRP007412_liver 0 .39 RPM 32 .80 RPM
SRP007412_testis 0 .00 RPM 54 .06 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1248 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1248 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1248 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1914
Gorilla gorilla retro_ggor_1400
Pongo abelii retro_pabe_1548
Callithrix jacchus retro_cjac_1146
Parental genes homology:
Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000151891 retrocopy
retro_cfam_1353,
Callithrix jacchus ENSCJAG000000068123 retrocopies
retro_cjac_1146, retro_cjac_1834, retro_cjac_3791,
Dasypus novemcinctus ENSDNOG000000101196 retrocopies
retro_dnov_1051, retro_dnov_1545, retro_dnov_170, retro_dnov_1890, retro_dnov_2044, retro_dnov_2255,
Echinops telfairi ENSETEG000000016755 retrocopies
retro_etel_1080, retro_etel_1162, retro_etel_1172, retro_etel_1887, retro_etel_2177,
Homo sapiens ENSG000000533722 retrocopies
retro_hsap_1766, retro_hsap_1914,
Gorilla gorilla ENSGGOG000000005332 retrocopies
retro_ggor_1400, retro_ggor_2244,
Macropus eugenii ENSMEUG000000000271 retrocopy
retro_meug_1606,
Microcebus murinus ENSMICG000000040192 retrocopies
retro_mmur_1235, retro_mmur_733,
Myotis lucifugus ENSMLUG000000015661 retrocopy
retro_mluc_374,
Macaca mulatta ENSMMUG000000066951 retrocopy
retro_mmul_107,
Monodelphis domestica ENSMODG000000158741 retrocopy
retro_mdom_1694,
Mustela putorius furoENSMPUG000000161812 retrocopies
retro_mputfur_1177, retro_mputfur_1430,
Mus musculus ENSMUSG000000287412 retrocopies
retro_mmus_852, retro_mmus_924,
Oryctolagus cuniculus ENSOCUG000000002742 retrocopies
retro_ocun_1191, retro_ocun_951,
Otolemur garnettii ENSOGAG000000107132 retrocopies
retro_ogar_1826, retro_ogar_2060,
Pongo abelii ENSPPYG000000017952 retrocopies
retro_pabe_1535, retro_pabe_1548,
Pan troglodytes ENSPTRG00000000262 2 retrocopies
retro_ptro_1182, retro_ptro_1248 ,
Rattus norvegicus ENSRNOG000000179791 retrocopy
retro_rnor_2967,
Ictidomys tridecemlineatus ENSSTOG000000281121 retrocopy
retro_itri_1551,
Tupaia belangeri ENSTBEG000000065028 retrocopies
retro_tbel_1020, retro_tbel_1189, retro_tbel_1210, retro_tbel_1873, retro_tbel_1945, retro_tbel_2665, retro_tbel_394, retro_tbel_559,


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