RetrogeneDB ID:

retro_pabe_2234

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:102076621..102077635(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EI24
Ensembl ID:ENSPPYG00000004033
Aliases:None
Description:etoposide induced 2.4 [Source:HGNC Symbol;Acc:13276]


Retrocopy-Parental alignment summary:






>retro_pabe_2234
ATGGCTGACAGTGTCAAAACCTTTCTCCAGGACCTTCCCAGGGGAGTCAAAGACTCCATCTGGGATATTTGTACCATCTC
CAGCTAGACGCTCCAATCCATCAAAAGAGAGGAGCAGCGTGGAAGAAGGGCAAGCATTGTCCTGGCACAGAGAATACTCC
AGAGTATAGAGTGGGAGCAAGCGAGTGAGCCAGCAAGTGTTGGTAGAATTTTCCAATGTTGCACTTGGAGTGGTGGAGTG
CTCTGGTTCAGTCTACTCTTGCTTATCGAGTGTTTATTCCTGGGCTTCAGTGAGTAACAGCGTGAATTACTTATGATCCA
TCACTGTGTGGAGATGCTTGGTCATGGCTGCAATTTTTCCTCGTATAAATTTCCAGGGCTTTTTGGATGCTCCCTTTGTT
CATGCCTAGCAAAGTTGTGAATGTCATTTGGTTCCAAGACACAGCTGACCTGGCATTTGAAGCATCAGGGAGGAAGCCTC
ACCCATTCCCTAGTGTCCACAAAATAACTGCTGACATGCTCTCCAATCTTTTGCTGCAGGCTCTTTTCCCCATTCAGGGA
AGGTCTGTGAGTCTCTTTCCCACCCATCTTGTTGGTCAGCTGGTTACTCTCTGGTGTTTGTCTCTTCTTGACTCATTCTA
CTGCTTCAAATATGGTTGGTTCAATAAAGGAATTGAAATGCACCAGCGGTTCCTCTAACATAGAGAGGAACTGGCTTTAC
TACTTTGGGTTTGGTTTGCCCTTGGCTTTTCTCACAGCAATGCAGTCCTCATATATTTTCCATGGCTGCCTTTTCTCTAT
CCTCTTTCCTTTATTCATTATCAGTGCAATGAGGCAAAGATCCCCGGCCAAGCATACCTCTTTGAGTTGCACCTCTCCTC
CTTCGTGGTCTTCTTAAGCAACAGACTCTTCCACAAGACACTCTCACCTGCAGTCTGCCTTGAGCAGCTCAACCTCTGCA
GAGAAGTTCCCTTCACCACATGTATCTCCACCCAAACTGAAGGCTACCGCAGGC

ORF - retro_pabe_2234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.1 %
Parental protein coverage: 99.71 %
Number of stop codons detected: 3
Number of frameshifts detected: 6


Retrocopy - Parental Gene Alignment:

ParentalMADSVKTFLQDLARGIKDSIWGICTIS-KLDARIQQKR-EEQRRRRASSVLAQRRAQSIERKQESEPRIV
MADSVKTFLQDL.RG.KDSIW.ICTIS..LDA.I.QKR.E...R.RAS.VLAQR..QSIE..Q.SEP..V
RetrocopyMADSVKTFLQDLPRGVKDSIWDICTIS<QLDAPIHQKR>EQRGR-RASIVLAQRILQSIEWEQASEPASV
ParentalSRIFQCCAWNGGVFWFSLLLF-YRVFIPVLQSVTARIIGDPSLHGDVWSWLEFFLTSVFSALWVLPLFVL
.RIFQCC.W.GGV.WFSLLL..YRVFIP.LQ.VTA.I..DPSL.GD.WSWL.FFL.....A.W.LPLF..
RetrocopyGRIFQCCTWSGGVLWFSLLLL<YRVFIPGLQ*VTA*ITYDPSLCGDAWSWLQFFLV*ISRAFWMLPLFMP
ParentalSKVVNAIWFQDIADLAFEVSGRKPHPFPSVSKIIADMLFNLLLQALFLIQGMFVSLFPIHLVGQLVSLLH
SKVVN.IWFQD.ADLAFE.SGRKPHPFPSV.KI.ADML.NLLLQALF.IQG..VSLFP.HLVGQLV.L..
RetrocopySKVVNVIWFQDTADLAFEASGRKPHPFPSVHKITADMLSNLLLQALFPIQGRSVSLFPTHLVGQLVTLWC
ParentalMSLLYSLYCFEYRWFNKGIEMHQRL-SNIERNWPYYFGFGLPLAFLTAMQSSYIISGCLFSILFPLFIIS
.SLL.S.YCF.Y.WFNKGIEMHQR..SNIERNW.YYFGFGLPLAFLTAMQSSYI..GCLFSILFPLFIIS
RetrocopyLSLLDSFYCFKYGWFNKGIEMHQRF>SNIERNWLYYFGFGLPLAFLTAMQSSYIFHGCLFSILFPLFIIS
ParentalA-NEAKTPGKAYLFQLRLFSLVVFLSNRLFHKTV-YLQSALSSSTSAEKFPSPHPSPAKLKAAAG
A.NEAK.PG.AYLF.L.L.S.VVFLSNRLFHKT...LQSALSSSTSAEKFPSPH.SP.KLKA.AG
RetrocopyA<NEAKIPGQAYLFELHLSSFVVFLSNRLFHKTL>HLQSALSSSTSAEKFPSPHVSPPKLKATAG

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 .00 RPM 55 .12 RPM
SRP007412_cerebellum 0 .00 RPM 51 .44 RPM
SRP007412_heart 0 .00 RPM 32 .84 RPM
SRP007412_kidney 0 .00 RPM 54 .39 RPM
SRP007412_liver 0 .00 RPM 76 .35 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_2234 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2234 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2234 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2782
Pan troglodytes retro_ptro_1883
Macaca mulatta retro_mmul_1443
Parental genes homology:
Parental genes homology involve 26 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009902 retrocopies
retro_amel_1449, retro_amel_1681,
Bos taurus ENSBTAG000000072022 retrocopies
retro_btau_1242, retro_btau_443,
Canis familiaris ENSCAFG000000108981 retrocopy
retro_cfam_1829,
Choloepus hoffmanni ENSCHOG000000126693 retrocopies
retro_chof_1433, retro_chof_1994, retro_chof_804,
Cavia porcellus ENSCPOG000000072722 retrocopies
retro_cpor_132, retro_cpor_929,
Dasypus novemcinctus ENSDNOG000000023624 retrocopies
retro_dnov_1083, retro_dnov_1421, retro_dnov_2143, retro_dnov_2345,
Equus caballus ENSECAG000000158611 retrocopy
retro_ecab_1022,
Erinaceus europaeus ENSEEUG000000032741 retrocopy
retro_eeur_435,
Felis catus ENSFCAG000000151001 retrocopy
retro_fcat_1754,
Homo sapiens ENSG000001495473 retrocopies
retro_hsap_236, retro_hsap_2782, retro_hsap_3804,
Loxodonta africana ENSLAFG0000001088815 retrocopies
retro_lafr_262, retro_lafr_263, retro_lafr_264, retro_lafr_265, retro_lafr_394, retro_lafr_395, retro_lafr_396, retro_lafr_397, retro_lafr_398, retro_lafr_399, retro_lafr_566, retro_lafr_589, retro_lafr_626, retro_lafr_627, retro_lafr_999,
Microcebus murinus ENSMICG000000030233 retrocopies
retro_mmur_398, retro_mmur_498, retro_mmur_632,
Myotis lucifugus ENSMLUG000000015831 retrocopy
retro_mluc_1249,
Macaca mulatta ENSMMUG000000100093 retrocopies
retro_mmul_1443, retro_mmul_1653, retro_mmul_2244,
Nomascus leucogenys ENSNLEG000000074513 retrocopies
retro_nleu_2149, retro_nleu_684, retro_nleu_853,
Oryctolagus cuniculus ENSOCUG000000146701 retrocopy
retro_ocun_1578,
Otolemur garnettii ENSOGAG000000018386 retrocopies
retro_ogar_1055, retro_ogar_1379, retro_ogar_2700, retro_ogar_2701, retro_ogar_659, retro_ogar_799,
Ochotona princeps ENSOPRG000000134912 retrocopies
retro_opri_106, retro_opri_1130,
Procavia capensis ENSPCAG000000127621 retrocopy
retro_pcap_452,
Pongo abelii ENSPPYG00000004033 3 retrocopies
retro_pabe_2234 , retro_pabe_3107, retro_pabe_416,
Pan troglodytes ENSPTRG000000044444 retrocopies
retro_ptro_1202, retro_ptro_1883, retro_ptro_206, retro_ptro_2581,
Pteropus vampyrus ENSPVAG000000045321 retrocopy
retro_pvam_1124,
Rattus norvegicus ENSRNOG000000303911 retrocopy
retro_rnor_2605,
Sarcophilus harrisii ENSSHAG000000173331 retrocopy
retro_shar_433,
Ictidomys tridecemlineatus ENSSTOG000000042992 retrocopies
retro_itri_1343, retro_itri_1373,
Tarsius syrichta ENSTSYG000000047472 retrocopies
retro_tsyr_1238, retro_tsyr_1423,


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