RetrogeneDB ID:

retro_pabe_2672

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:100132391..100133589(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CRLF3
Ensembl ID:ENSPPYG00000008142
Aliases:None
Description:cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]


Retrocopy-Parental alignment summary:






>retro_pabe_2672
CTGTGGGAGGCACAGAGGCAGATCAAGGAGTGTGCACCACAGACAAAGGATGTTCTTAAACAGCATTTTAATGATTTAAA
GGGAACCCTTGAGGAGCTCCTGGATGAGCGATTGGTGACCCTTTAGCAAGAGGTGGACATCGTTGAGCAGGAGACCATTA
AACCATTAGATGACTGCCAGAGGCTCATAGAACACGGAGTCAACACTGCAGAGGACTTAGTCTGAGTAGGTGAGATTGCC
ATGGTTGGTAGTGTAGAAGAGAATGAGCAACAGTATAGCTTTACCAAAAAGGTCTCACACATTCAGTTGGACAGCTTACC
AGAAGTACCTTTACTGGTTGATGTGCTTTGTTTATCTGCTCAGTTGGATGACTCAATTCTTATAGTAAAAGACTACATTT
CTAAGCATGGAACAGTAGCATCTCTCCCACCAGTACAGATATAAGAACTGATACAGAAACCTGGAGTCATCACAGTAGGA
TGGTGTAAGGTGGATGATGATTTTACAGCCCAAGATTATAGGCTCTAATTTTGTAAATGTACTTCAAATCATTATGAGGA
TGTACATGTAGGTTCTGAAACTCAATTCATAGTACTGCACATGGACTCCAATGTTGATTATCAGTTCAATGTCTGCACCT
GAGGAGATGGTCAACAGGAGTGCAGCCCCGAAGTGTCCCCCAGATAGGTCATTTCACATTGATGCCTCATGAGTGGACAG
CTGGTTTTGAGGGGTACAGTCTGAAAGTCGAAGTAATATTGCATTCTGGAATGATTCTCAATCCTCAGGTGTTCTCTACT
CTAGAACTCCAACTTATTTCTGTGGGCAGACATTAACATTCAGAGTTGAAATTGTGGGACAGAAGAGACAGTACGGGGTG
TTTGCAGAAAGACGGAATGGATATGACTCTCTGCAGCAGGATCAAGCTATATGTATGAGTACAAACGGTGAAGTTTTTGT
TAATGGAAAAGAAATGACTAATGAGTTAACTTCAGTTACTTCTGGGTGCACTGTCACATTTGACATTGAAGCTGTCACTC
TAGGAACCACCAATAATAATGAAGGCAGGAACTTCAAGCTTCGAGTAACAATTAGCTCAAATAACAGAGAAGTGGTTTTT
AATTAGTTACTCGATCAATCTTGTGGTTCTCTTTACTTTGGATGCTCATTTTTCCATCCTGGATGGAAAATATTAGTG

ORF - retro_pabe_2672 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.34 %
Parental protein coverage: 91.63 %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLREARRQIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTA
L.EA.RQIKE.A.QT.DVLKQHFNDLKGTL..LLDERLVTL.QEVD..EQETIKPLDDCQ.LIEHGVNTA
RetrocopyLWEAQRQIKECAPQTKDVLKQHFNDLKGTLEELLDERLVTL*QEVDIVEQETIKPLDDCQRLIEHGVNTA
ParentalEDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGT
EDLV..GEIAM.G.V.EENE...SFTKK.SHIQLDSLPEVPLLVDV.CLSAQLDDSIL.IVKD.I.KHGT
RetrocopyEDLV*VGEIAMVGSV-EENEQQYSFTKKVSHIQLDSLPEVPLLVDVLCLSAQLDDSIL-IVKDYISKHGT
ParentalVASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQ
VAS.PPVQI.ELI.KPG.I.V.WCKVDDDFTAQDYRL.F.KCTSNH.EDV.VGSET.FIVLH.D.NVDYQ
RetrocopyVASLPPVQI*ELIQKPGVITVGWCKVDDDFTAQDYRL*FCKCTSNHYEDVHVGSETQFIVLHMDSNVDYQ
ParentalFRVCARGDGRQEWS-PWSVPQIGHSTLVPHEWTAGFEGYSL-SSRRNIALRNDSESSGVLYSRAPTYFCG
F.VC..GDG.QE.S.P.SVPQIGH.TL.PHEWTAGFEGYSL..SR.NIA..NDS.SSGVLYSR.PTYFCG
RetrocopyFNVCT*GDGQQECS<PRSVPQIGHFTLMPHEWTAGFEGYSL<ESRSNIAFWNDSQSSGVLYSRTPTYFCG
ParentalQTLTFRVETVGQPDRRDSIGVCAEKQDGYDSLQRDQAVCISTNGAVFVNGKEMTNQLPAVTSGSTVTFDI
QTLTFRVE.VGQ.......GV.AE...GYDSLQ.DQA.C.STNG.VFVNGKEMTN.L..VTSG.TVTFDI
RetrocopyQTLTFRVEIVGQ---KRQYGVFAERRNGYDSLQQDQAICMSTNGEVFVNGKEMTNELTSVTSGCTVTFDI
ParentalEAVTLGTTSNNEGGHFKLRVTISSNNREVVFDWLLDQSCGSLYFGCSFFYPGWKVLV
EAVTLGTT.NNEG..FKLRVTISSNNREVVF..LLDQSCGSLYFGCSFF.PGWK.LV
RetrocopyEAVTLGTTNNNEGRNFKLRVTISSNNREVVFN*LLDQSCGSLYFGCSFFHPGWKILV

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_prefrontal_cortex 0 .00 RPM 12 .55 RPM
SRP007412_cerebellum 0 .00 RPM 17 .75 RPM
SRP007412_heart 0 .00 RPM 4 .61 RPM
SRP007412_kidney 0 .00 RPM 5 .70 RPM
SRP007412_liver 0 .00 RPM 5 .42 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2672 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2672 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2672 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3360
Pan troglodytes retro_ptro_2175
Gorilla gorilla retro_ggor_2278

Parental genes homology:
Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000141631 retrocopy
Homo sapiens ENSG000001763903 retrocopies
Gorilla gorilla ENSGGOG000000050023 retrocopies
Macaca mulatta ENSMMUG000000090692 retrocopies
Mus musculus ENSMUSG000000175611 retrocopy
Nomascus leucogenys ENSNLEG000000058504 retrocopies
Pongo abelii ENSPPYG00000008142 3 retrocopies
retro_pabe_1925, retro_pabe_1984, retro_pabe_2672 ,
Pan troglodytes ENSPTRG000000089632 retrocopies



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