RetrogeneDB ID:

retro_sscr_494

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:15:36618258..36619287(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000025461
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM185A
Ensembl ID:ENSSSCG00000012739
Aliases:None
Description:transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]


Retrocopy-Parental alignment summary:






>retro_sscr_494
GATTTCAACCCGAGTAAGTTCCTCATCTACGCCTGTCTGCTGCTCTTCTCCGTGCTGCTGCCCCTCCGCCTGGACGGCGT
CATCCAGTGGAGCTATTGGGCTGTGTTCGCCCCCATATGGCTGTGGAAGCTCCTGGTCCTTGCTGGCGCCTCGGTGGGCG
CGGGCGTTTGGGCGAGGAATCCCCGTTACCGCACCGAGGGTGAGGCCTGTGTGGAGTTCAAGGCCATGCTGATCGCCGTG
GGCATCCACCTGCTGCTACTCATGTTCGAAGTCCTAGTCTGCGACAGGGTGGAGAGGGGCACCCACTTCTGGCTACTGGT
CTTCATGCCGCTCTTCTTTGTGTCTCCCGTCTCCGTGGCCGCTTGCGTATGGGGCTTCCGGCACGACAGGTCCCTGGAGC
TGGAGATCCTGTGCTCTGTCAACATCCTGCAGTTCATCTTCATCGCCCTGAGGCTGGACAGGATCATCCACTGGCCGTGG
CTGGTGGTGTTTGTGCCGCTCTGGATCCTCATGTCCTTTCTCTGCTTGGTGGTCCTCTATTACATTGTCTGGTCCCTCCT
GTTCCTGCGTTCTCTGGATGTGGTTGCCGAGCAGCGAAGAACACATGTGACCATGGCCATCAGCTGGATAACGATCGTCG
TGCCCCTGCTCACTTTTGAGGTTCTGCTGGTTCACAGGCTGGACGGCCACAACGTGTTCTCCTACGTCTCCATATTCGTC
CCTCTTTGGCTGTCATTAATCACTTTAATGACCACAACATTTCGGCGAAAGGGGGGCAACCACTGGTGGTTTGGTATTCG
CAGAGATTTCTGTCAGTTTTTGCTTGAAATTTGCCCTTGTTTAAGAGAATACGGGAACATTTCATACGATCTACATCATG
AAGATAGTGAAGACGCTGAAGAAACGTCATCTGTTCCAGAAGCTCCTAAAATCGCTCCAATGTTCGGAAAGAAGGCCAGG
GTCGTGATAACCCAGAGCCCTGGAAAATATGTTCCCCCACCTCCCAAGTTAAATATTGATATGCCGGAT

ORF - retro_sscr_494 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.46 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEGETC
DF.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.YR.EGE.C
RetrocopyDFNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVLAGASVGAGVWARNPRYRTEGEAC
ParentalVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSV
VEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSV
RetrocopyVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSV
ParentalNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVLAEQRRTHITMALSWM
NILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.SW.
RetrocopyNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAISWI
ParentalTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEVFPF
TIVVPLLTFE.LLVH.LDGHN.FS...IFVPLWLSLITLM.TTF..KGGNHWWFGIR.DFCQFLLE..P.
RetrocopyTIVVPLLTFEVLLVHRLDGHNVFSYVSIFVPLWLSLITLMTTTFRRKGGNHWWFGIRRDFCQFLLEICPC
ParentalLREYGNISYDLHHEENEETEET-PVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
LREYGNISYDLHHE..E..EET..VPE.PKIAPMF.KKARVVITQSPGKYV.PPPKLNI.MPD
RetrocopyLREYGNISYDLHHEDSEDAEETSSVPEAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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
SRP014902_placenta 11 .41 RPM 63 .58 RPM
SRP014902_testis 12 .16 RPM 31 .26 RPM
SRP018288_heart 5 .19 RPM 10 .19 RPM
SRP018288_kidney 3 .64 RPM 14 .58 RPM
SRP018288_liver 3 .36 RPM 4 .16 RPM
SRP018288_lung 5 .50 RPM 18 .23 RPM
SRP018856_adipose 16 .96 RPM 60 .21 RPM
SRP035408_brain 5 .11 RPM 13 .72 RPM
SRP035408_liver 2 .00 RPM 3 .38 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_494 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_494 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_494 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_1
Equus caballus retro_ecab_426
Parental genes homology:
Parental genes homology involve 22 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
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,
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,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG00000012739 1 retrocopy
retro_sscr_494 ,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,




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