RetrogeneDB ID:

retro_pabe_118

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2b:14290772..14291825(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000012782
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM185A
Ensembl ID:ENSPPYG00000020809
Aliases:TMEM185A, FAM11A
Description:transmembrane protein 185A [Source:RefSeq peptide;Acc:NP_001126120]


Retrocopy-Parental alignment summary:






>retro_pabe_118
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCCAGTAAGTTTCTCATCTATACCTGCCTGCTGCTCTTCTCGGTGCT
GCTGCCCCTCCGCCTGGACGGCATCATCCAATGGAGCTACTGGGCCGTCTTTGCCCCCATATGGCTGTGGAAGCTTCTAG
TCGTCGCAGGCGCCTCCGTGGGCGCGGGCGTTTGGGCCCGCAACCCTCGCTACCGCACCGAGGGAGAGGCCTGTGTGGAG
TTCAAAGCCATGCTGATCGCTGTGGTCATCCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAG
GGGCACCCACTTCTGGCTGCTGGTCTTCATGCCTCTCTTCTTCGTGTCCCCCGTGTCCGTGGCTGCCTGCGTCTGGGGCT
TTCGACACGATAGGTCGCTGGAGCTGGAGATCCTGTGCTCGGTCAACATACTGCAGTTCATCTTCATCGCCCTAAAGCTG
GACAGGATTATTCACTGGCCGTGGCTAGTGGTGTTTGTGCCCCTGTGGATCCTCATGTCGTTCCTTTGCCTGGTCGTTCT
CTATTACATCGTCTGGTCCCTCCTGTTCCTGCGGTCCCTGGATGTGGTTGCCGAGCAGCGAAGAACACACGTGACCATGG
CTATCAGTTGGATAACGATTGTCGTGCCTCTGCTCACTTTTGAGGTCCTGCTCGTTCACAGATTGGATGGCCACAATACA
TTCTCCTACGTCTCCATATTTGTTCCCCTTTGGCTTTCCTTACTAACTTTAATGGCCACAACATTTAGGCGAAAGGGGGG
CAATCATTGGTGGTTTGGCATTCGCAGAGACTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGGA
ACATTTCATATGATCTCCATCACGAAGATAGTGAAGATGCTGAAGAAACATCAGTTCCAGAAGCTCCGAAAATTGCTCCA
ATATTTGGAAAGAAGGCCAGAGTAGTTATAACCCAGAGCCCTGGGAAATACGTTCCCCCCCCTCCCAAGTTAAATATTGA
TATGCCAGATTAA

ORF - retro_pabe_118 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.29 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
MN.RGLFQDFNPSKFLIY.CLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.
RetrocopyMNPRGLFQDFNPSKFLIYTCLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVVAGASVGAGVWARNPR
ParentalYRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
YR.EGE.CVEFKAMLIAV.IHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
RetrocopyYRTEGEACVEFKAMLIAVVIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
ParentalELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
ELEILCSVNILQFIFIAL.LD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
RetrocopyELEILCSVNILQFIFIALKLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH
ParentalITMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
.TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS...IFVPLWLSL.TLMATTF..KGGNHWWFGIR.DFCQ
RetrocopyVTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYVSIFVPLWLSLLTLMATTFRRKGGNHWWFGIRRDFCQ
ParentalFLLEIFPFLREYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
FLLEIFPFLREYGNISYDLHHED.E..EET.VPE.PKIAP.F.KKARVVITQSPGKYV.PPPKLNI.MPD
RetrocopyFLLEIFPFLREYGNISYDLHHEDSEDAEETSVPEAPKIAPIFGKKARVVITQSPGKYVPPPPKLNIDMPD

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 5 .42 RPM 7 .57 RPM
SRP007412_cerebellum 3 .16 RPM 5 .96 RPM
SRP007412_heart 4 .40 RPM 4 .27 RPM
SRP007412_kidney 9 .41 RPM 3 .18 RPM
SRP007412_liver 4 .16 RPM 1 .56 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_118 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_118 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_118 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_104
Gorilla gorilla retro_ggor_189
Macaca mulatta retro_mmul_310
Mus musculus retro_mmus_358
Rattus norvegicus retro_rnor_6
Parental genes homology:
Parental genes homology involve 26 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Cavia porcellus ENSCPOG000000036221 retrocopy
retro_cpor_5,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG00000020809 1 retrocopy
retro_pabe_118 ,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


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