RetrogeneDB ID:

retro_pabe_158

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:11:100405754..100406945(+)
Located in intron of:ENSPPYG00000003821
Retrocopy
information
Ensembl ID:ENSPPYG00000003822
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DDI2
Ensembl ID:ENSPPYG00000001841
Aliases:None
Description:DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]


Retrocopy-Parental alignment summary:






>retro_pabe_158
ATGCTGATCACCGTGTACTGTGTGCGGAGGGACCTATCCGAGGTCACCTTCTCTCTCCAGGTCAGCCCCGACTTTGAGCT
CCGAAACTTCAAGGTCCTCTGTGAGGCGGAGTCCAGAGTTCCTGCCGAAGAGATCCAGATCATCCACATGGAGCGACTCC
TCATCGAGGACCACTGTTCCCTGGGCTCCTACGGCCTCAAAGATGGCGATATCGTGGTTTTACTGCAGAAGGACAATGTG
GGACCTCGGGCTCCAGGGCGTGCCCCGAACCAGCCTCGTATAGACTTCAGCGGCATTGCGGTGCCCGGGACGTCCAGCTC
CTGTCCGCAGCACCCTGGACAGCAGCAGCAGCGCACACCCGCTGCCCAGCGGTCACATGGCTTGGCGTCAGGAGAGACGG
TGGCCGGCCCGCAAGGTCTGGGCAGCCCTGCCCTGATCCGCAGCATGCTGCTCTCCAACCCGCACGATCTGTCCCTGCTC
AAGGAACGCAACCCTCCCTTGGCAGAAGCCCTGCTCAGTGGAAGCCTTGAGACCTTTTCTCAGGTGCTGATGGAGCAGCA
AAGAGAAAAGGCCTTGAGAGAGCAAGAGAGGCTTTGTCTCTACATGGCCGACCCACTGGATTCGGAAGCTCAGGCCAAAA
TAGAAGAGGAAATCCGGCAGCAGAACATTGAAGAAAACATGAATATAGCAATAGAAGAGGCCCCCGAGAGTTTCGGACAA
GTGACGATGCTCTACATTAACTGCAAAGTGAATGGGCATCCTTTGAAGGCTTTTGTTGACTCGGGCGCCCAGATGACCAT
TATGAGCCAGGCTTGTGCCGAGCAATGTAACATCATGAGGCTGGTGGACCGACGGTGGGCTGGGGTTGCTAAAGGAGTGG
GCACACAGAGAATTATTGGCCGTGTTCATCTAGCTCAGATTCAAATTGAAGGTGATTTCTTACAGTGCTCTTTCTCCATA
CTTGAGGATCAACCCATGGATATGCTTCTAGGCCTAGATATGCTCCGGAGACATCAATGTTCCATCGATTTGAAGAAAAA
TGTGCTGGTCATCGGCACCACTGGCACGCAGACTTACTTTCTTCCTGAGGGAGAGTTGCCCTTATGCTCTAGGATGGTAA
ATGGGCAAGATGAGTCTTCGGACAAGGAAATTACACATTCGGTCATGGATTCAGAACGAAAAGAGCATTAA

ORF - retro_pabe_158 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.45 %
Parental protein coverage: 73.43 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRQKENADPRPPVQFPNLPRIDFSSIAVPGTSSPRQRQPPGTQQSHS-SPGEITSSPQGLDNPALLRDMLL
R....A...P...F.........S...P......Q...P..Q.SH....GE....PQGL..PAL.R.MLL
RetrocopyRAPGRAPNQPRIDFSGIA-VPGTSSSCPQHPGQQQQRTPAAQRSHGLASGETVAGPQGLGSPALIRSMLL
ParentalANPHELSLLKERNPPLAEALLSGDLEKFSRVLVEQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQ
.NPH.LSLLKERNPPLAEALLSG.LE.FS.VL.EQQ...A.REQER..L..ADP.D.EAQAKIEE.IRQQ
RetrocopySNPHDLSLLKERNPPLAEALLSGSLETFSQVLMEQQREKALREQERLCLYMADPLDSEAQAKIEEEIRQQ
ParentalNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAK
NIEENM.IA.EEAPESFGQV.MLYINCKVNGHP.KAFVDSGAQMTIMSQACAE.CNIMRLVDRRWAG.AK
RetrocopyNIEENMNIAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAEQCNIMRLVDRRWAGVAK
ParentalGVGTQKIIGRVHLAQVQIEGDFLPCSFSILEEQPMDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTTFL
GVGTQ.IIGRVHLAQ.QIEGDFL.CSFSILE.QPMDMLLGLDML.RHQCSIDLKKNVLVIGTTG.QT.FL
RetrocopyGVGTQRIIGRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSIDLKKNVLVIGTTGTQTYFL
ParentalPEGELPECARLAYG
PEGELP.C.R...G
RetrocopyPEGELPLCSRMVNG

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 5 .64 RPM
SRP007412_cerebellum 0 .00 RPM 8 .39 RPM
SRP007412_heart 0 .12 RPM 3 .91 RPM
SRP007412_kidney 0 .03 RPM 6 .36 RPM
SRP007412_liver 0 .03 RPM 9 .18 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_158 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_158 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_158 has 11 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_96
Pan troglodytes retro_ptro_570
Gorilla gorilla retro_ggor_143
Macaca mulatta retro_mmul_231
Callithrix jacchus retro_cjac_196
Mus musculus retro_mmus_67
Oryctolagus cuniculus retro_ocun_249
Bos taurus retro_btau_15
Sus scrofa retro_sscr_6
Canis familiaris retro_cfam_193
Equus caballus retro_ecab_110
Parental genes homology:
Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118731 retrocopy
retro_amel_10,
Bos taurus ENSBTAG000000187182 retrocopies
retro_btau_15, retro_btau_650,
Canis familiaris ENSCAFG000000162201 retrocopy
retro_cfam_193,
Callithrix jacchus ENSCJAG000000086251 retrocopy
retro_cjac_196,
Cavia porcellus ENSCPOG000000208851 retrocopy
retro_cpor_88,
Equus caballus ENSECAG000000007621 retrocopy
retro_ecab_110,
Homo sapiens ENSG000001973121 retrocopy
retro_hsap_96,
Gorilla gorilla ENSGGOG000000135371 retrocopy
retro_ggor_143,
Macropus eugenii ENSMEUG000000061481 retrocopy
retro_meug_1364,
Myotis lucifugus ENSMLUG000000306691 retrocopy
retro_mluc_68,
Macaca mulatta ENSMMUG000000199121 retrocopy
retro_mmul_231,
Monodelphis domestica ENSMODG000000035151 retrocopy
retro_mdom_282,
Mustela putorius furoENSMPUG000000163321 retrocopy
retro_mputfur_1509,
Mus musculus ENSMUSG000000785151 retrocopy
retro_mmus_67,
Oryctolagus cuniculus ENSOCUG000000238911 retrocopy
retro_ocun_249,
Otolemur garnettii ENSOGAG000000277091 retrocopy
retro_ogar_4,
Ochotona princeps ENSOPRG000000184481 retrocopy
retro_opri_4,
Pongo abelii ENSPPYG00000001841 1 retrocopy
retro_pabe_158 ,
Pan troglodytes ENSPTRG000000240591 retrocopy
retro_ptro_570,
Pteropus vampyrus ENSPVAG000000050841 retrocopy
retro_pvam_420,
Rattus norvegicus ENSRNOG000000122741 retrocopy
retro_rnor_2606,
Sus scrofa ENSSSCG000000034621 retrocopy
retro_sscr_6,
Ictidomys tridecemlineatus ENSSTOG000000194471 retrocopy
retro_itri_93,
Tarsius syrichta ENSTSYG000000025221 retrocopy
retro_tsyr_1120,


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