RetrogeneDB ID:

retro_pabe_1883

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:22:27439088..27439873(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000011749
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA1
Ensembl ID:ENSPPYG00000003466
Aliases:None
Description:proteasome subunit alpha type-1 [Source:RefSeq peptide;Acc:NP_001124812]


Retrocopy-Parental alignment summary:






>retro_pabe_1883
TTTCGAAATCAGTATGACAATGAAGTCACTGTTTGGAGCCCTCAGGGCAGGATTCATCAAATTGAATATGCAATGGAAGC
TGTTAAACAAGGTTCAGCCACAGTTGGTCTGAAATCAAAAACTCATGGAGTGTTGGTTGCATTGAAAAGGGCACAATCAG
AGCTTGCAGCTCATCAGAAAAAAATTCTCCATGTTGACAACCATATTGGTATCTCAATTGCAGGGCTTACTGCTGATGCT
AGACTGTTAGTAATTTTATGCGTCAGGAGTGTTTGGATTCCAGATTTGTATTCGATAGACCACTGCCTGTGTCTCGTCTT
GTATCTCTAATTGGAAGCAAGACCCAGATACCAACACAACGATATGGCCGGAGACCATATGGTGTTGGGCTGCTTATTGC
TGGTTATGATGATATCGGCCCTCACATTTTCCAAACCTGTCCATCTGCTAACTACTTTGACTGCAGAGCCATGTCCATTG
GAGCCCTTTCCCAATCAGCTCGTACTTACTTAGAGAGACATACGTCTGAATTTATGGAGTGCAATTTAAATGAACCAGTT
AAACATGGTCTGCGTGCCTTAAGAGAGACACTTCCTGCAGAACAGGACCTGACTACAAAGAATGTTTCCACTGGAATTGT
TGGTAAAGACTTGGAGTTTACAATCTATGATGATGATGATGTGTCTCCATTCCTGGAAGGTCTTGAAGAAAGACCACAGA
GAAAGGCACAGCCTGCTCAACCTGCTGATGAACCTGCAGAAAAGGCTGATGAACCAATGGAACAT

ORF - retro_pabe_1883 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.58 %
Parental protein coverage: 99.62 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKILHVDNHIG
FRNQYDN.VTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTH.VLVALKRAQSELAAHQKKILHVDNHIG
RetrocopyFRNQYDNEVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHGVLVALKRAQSELAAHQKKILHVDNHIG
ParentalISIAGLTADARLLC-NFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM
ISIAGLTADARLL..NFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDD.
RetrocopyISIAGLTADARLLV<NFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDI
ParentalGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNV
GPHIFQTCPSANYFDCRAMSIGA.SQSARTYLERH.SEFMECNLNE.VKHGLRALRETLPAEQDLTTKNV
RetrocopyGPHIFQTCPSANYFDCRAMSIGALSQSARTYLERHTSEFMECNLNEPVKHGLRALRETLPAEQDLTTKNV
ParentalSIGIVGKDLEFTIYDDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH
S.GIVGKDLEFTIYDDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH
RetrocopySTGIVGKDLEFTIYDDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH

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 .22 RPM 34 .22 RPM
SRP007412_cerebellum 0 .12 RPM 31 .74 RPM
SRP007412_heart 0 .18 RPM 26 .40 RPM
SRP007412_kidney 0 .10 RPM 31 .56 RPM
SRP007412_liver 0 .18 RPM 38 .31 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_1883 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1883 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1883 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024402 retrocopies
retro_amel_1733, retro_amel_1903,
Bos taurus ENSBTAG000000065641 retrocopy
retro_btau_1833,
Choloepus hoffmanni ENSCHOG0000000539511 retrocopies
retro_chof_155, retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus ENSECAG000000240861 retrocopy
retro_ecab_1078,
Felis catus ENSFCAG000000113811 retrocopy
retro_fcat_972,
Homo sapiens ENSG000001290841 retrocopy
retro_hsap_4720,
Gorilla gorilla ENSGGOG000000014161 retrocopy
retro_ggor_2933,
Macropus eugenii ENSMEUG000000111121 retrocopy
retro_meug_71,
Myotis lucifugus ENSMLUG000000092514 retrocopies
retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta ENSMMUG000000164461 retrocopy
retro_mmul_2509,
Mustela putorius furoENSMPUG000000131994 retrocopies
retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus ENSMUSG000000307511 retrocopy
retro_mmus_831,
Oryctolagus cuniculus ENSOCUG000000004392 retrocopies
retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii ENSOGAG000000116223 retrocopies
retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps ENSOPRG000000136771 retrocopy
retro_opri_370,
Pongo abelii ENSPPYG00000003466 2 retrocopies
retro_pabe_1883 , retro_pabe_3664,
Pan troglodytes ENSPTRG000000033851 retrocopy
retro_ptro_3137,
Sarcophilus harrisii ENSSHAG000000156261 retrocopy
retro_shar_217,
Ictidomys tridecemlineatus ENSSTOG000000062702 retrocopies
retro_itri_1470, retro_itri_987,
Tupaia belangeri ENSTBEG000000120373 retrocopies
retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta ENSTSYG000000038692 retrocopies
retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos ENSVPAG000000088203 retrocopies
retro_vpac_344, retro_vpac_648, retro_vpac_82,


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