RetrogeneDB ID:

retro_mmul_1412

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:2:11565055..11565824(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.3111
Ensembl ID:ENSMMUG00000002163
Aliases:None
Description:keratin, type II cytoskeletal 8 [Source:RefSeq peptide;Acc:NP_001247474]


Retrocopy-Parental alignment summary:






>retro_mmul_1412
AGGCAGCTGTATGAAGAGGAGATCCAGGAGCTGTCCCAGATCTTGGACACATCTGTGGTTTTGCTCATGGACAACAGCTG
CTCCCCGGACATGGACAGCATCATCGCCCAGGTCAAGGCCCAGTATGAAGAGATCGCCAACCGCAGCCAGGCCAAGGCTG
AGAGCATGTACCAGATCAAGTATGAGGAGCTACAGACGCTTGCTGGGAAGCATGGGGATGACCTGCATCATACAAAGATG
GAGATCTCTGAGATGAACTGGAACATCAGCTGACTCCAGCCTGACACAGAGGGCTTCAAAGGCCAGAGGGCTTCCCCGGA
GGCCACCACAGATCCTGAGCAGCATGGGGAGCTGACGGTTAAGAATGCCAACACCAAGCTGTATGATCTGGGGCCCGCCT
GCAGTGGGCCAAGCAGGACATGGTGCAGCAGCTGCATGAGTGCCAGGAGCTGATGAAATCAAGCTGGCTCTGGACATTGA
GATTGCCACCTACAGGAAGCTGCTGGAGGGCGTGGAGAGCTGGCTGGAGTCAGGGATGCAGAACATGAGTATCCATATGA
AGACCACTGGTGGCTATGCAGGTGGGCTGAGCTCAGCTTATGGGGACCTCACAAGCCCCAGCCTCAACTATGGCCTGGGC
TTCAGCTTTGGCTCCGGCATGGGCTCCACCTCCTTCAGCTGCACCTGCTCCATCAGGGCCATGGTTACGAAGAGGATCAA
GACCCACAATGGAAAGCTGGTGTCCAAGTCCTCTGATGTCCTGCCAAAG

ORF - retro_mmul_1412 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.25 %
Parental protein coverage: 53.62 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRQLYEEEIRELQSQISDTSVVLSMDNSRSLDMDSIIAEVKAQYEEIANRSRAEAESMYQIKYEELQSLAG
RQLYEEEI.EL.SQI.DTSVVL.MDNS.S.DMDSIIA.VKAQYEEIANRS.A.AESMYQIKYEELQ.LAG
RetrocopyRQLYEEEIQEL-SQILDTSVVLLMDNSCSPDMDSIIAQVKAQYEEIANRSQAKAESMYQIKYEELQTLAG
ParentalKHGDDLRRTKTEISEMNRNISRLQAEIEGLKGQRASLEAAIADAEQRGELAIKDANAKLSELEAA-LQRA
KHGDDL..TK.EISEMN.NIS.LQ...EG.KGQRAS.EA...D.EQ.GEL..K.AN.KL..L..A.LQ.A
RetrocopyKHGDDLHHTKMEISEMNWNIS*LQPDTEGFKGQRASPEAT-TDPEQHGELTVKNANTKLYDLGPA<LQWA
ParentalKQDMARQLREYQELMN-VKLALDIEIATYRKLLEGEESRLESGMQNMSIHTKTTSGYAGGLSSAYGGLTS
KQDM..QL.E.QELM...KLALDIEIATYRKLLEG.ES.LESGMQNMSIH.KTT.GYAGGLSSAYG.LTS
RetrocopyKQDMVQQLHECQELMK<IKLALDIEIATYRKLLEGVESWLESGMQNMSIHMKTTGGYAGGLSSAYGDLTS
ParentalPGLSYGLGSSFGSGAGSSSFSRTSSSRAVVVKKIETRDGKLVSESSDVLPK
P.L.YGLG.SFGSG.GS.SFS.T.S.RA.V.K.I.T..GKLVS.SSDVLPK
RetrocopyPSLNYGLGFSFGSGMGSTSFSCTCSIRAMVTKRIKTHNGKLVSKSSDVLPK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 0 .11 RPM 0 .00 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 0 .24 RPM
SRP007412_cerebellum 0 .06 RPM 0 .06 RPM
SRP007412_heart 0 .65 RPM 8 .24 RPM
SRP007412_kidney 0 .23 RPM 22 .18 RPM
SRP007412_liver 0 .04 RPM 33 .41 RPM
SRP007412_testis 0 .04 RPM 0 .94 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1412 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1412 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1412 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 151 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000071992 retrocopies
Callithrix jacchus ENSCJAG000000181473 retrocopies
Cavia porcellus ENSCPOG000000026155 retrocopies
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
Felis catus ENSFCAG000000002982 retrocopies
Homo sapiens ENSG0000017042128 retrocopies
Gorilla gorilla ENSGGOG0000001467318 retrocopies
Macaca mulatta ENSMMUG00000002163 22 retrocopies
Mustela putorius furoENSMPUG000000064417 retrocopies
Mus musculus ENSMUSG000000493821 retrocopy
Nomascus leucogenys ENSNLEG000000177338 retrocopies
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
Otolemur garnettii ENSOGAG0000001174016 retrocopies
Pongo abelii ENSPPYG0000000456231 retrocopies
Pteropus vampyrus ENSPVAG000000093603 retrocopies
Rattus norvegicus ENSRNOG000000097791 retrocopy



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