RetrogeneDB ID:

retro_pabe_1433

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:17:15675399..15675949(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSPPYG00000014675
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_1433
ATGAAGACCGCTCTCAGCAATCAGACTGCTAACATTCTAGAAAATGTCGACATTACTCTGAAGGGACACACAGTTATCGT
GAAGGGCCCCAGAGGGACTTCAATCGCATCAGTGTAGAACTGAGTCTTCTTGGAAAGAAAACAAAAAAGGCTCCGGGTTG
ACAAATGGTGGGGTAACGGAAAAGAACTGCTACTGTTCGGACTATTTTACTCATGTACAGAACATGATCAAGGGTGTCAC
ACTGGACTTCCATTACAAGTTAAGGTCTGTGTATGCTCACTTCCCCATCAACGTTGTTATTCAGGAGAATGGGTCTCCTG
TTGAAATCCAAAATTTCTTGGGTGAAAAATACATCCGCAGGGTTCGGATGAGACCAGGTGTTGCTTGTTCAGTATCTCAA
ACCCAGAAAGATGAAGGAAACGACATTGAGCTTGTTTCAAATTCAGCGGCTTTGATTCAGCAAGCCACAACAGTTAAAAA
CAAGGCAATCAGGAAATTTTTGGATGGTATATATGTCTCTGAAAAAGGAACTGTTCAGCAGGCTGATGAA

ORF - retro_pabe_1433 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.67 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMKTILSNQTVDIPENVDITLKGRTVIV-KGPRGTLRRDFNHINVELSLLGKK-KKRLRVDKWWGNRKEL-
MKT.LSNQT..I.ENVDITLKG.TVIV..GP.....RDFN.I.VELSLLGKK..KRLRVDKWWGN.KEL.
RetrocopyMKTALSNQTANILENVDITLKGHTVIV<EGPQ----RDFNRISVELSLLGKK>QKRLRVDKWWGNGKEL<
ParentalATVRTIC-SHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSV
ATVRTI...HVQNMIKGVTL.F.YK.RSVYAHFPINVVIQENGS.VEI.NFLGEKYIRRVRMRPGVACSV
RetrocopyATVRTIL<THVQNMIKGVTLDFHYKLRSVYAHFPINVVIQENGSPVEIQNFLGEKYIRRVRMRPGVACSV
ParentalSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIYVSEKGTVQQADE
SQ.QKDE....GNDIELVSNSAALIQQATTVKNK.IRKFLDGIYVSEKGTVQQADE
RetrocopySQTQKDE----GNDIELVSNSAALIQQATTVKNKAIRKFLDGIYVSEKGTVQQADE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .06 RPM 36 .05 RPM
SRP007412_cerebellum 0 .00 RPM 52 .77 RPM
SRP007412_heart 0 .00 RPM 52 .29 RPM
SRP007412_kidney 0 .07 RPM 97 .75 RPM
SRP007412_liver 0 .03 RPM 100 .40 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1433 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1433 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1433 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1717
Gorilla gorilla retro_ggor_1286
Callithrix jacchus retro_cjac_2621

Parental genes homology:
Parental genes homology involve 29 parental genes, and 555 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000318731 retrocopies
Bos taurus ENSBTAG000000145183 retrocopies
Canis familiaris ENSCAFG0000001600828 retrocopies
Callithrix jacchus ENSCJAG0000000072329 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Equus caballus ENSECAG000000164897 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Felis catus ENSFCAG0000001228434 retrocopies
Homo sapiens ENSG0000016368228 retrocopies
Gorilla gorilla ENSGGOG0000002279926 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Loxodonta africana ENSLAFG0000001202138 retrocopies
Macropus eugenii ENSMEUG000000167228 retrocopies
Microcebus murinus ENSMICG0000001677818 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Macaca mulatta ENSMMUG0000000855322 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Nomascus leucogenys ENSNLEG0000001710026 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Procavia capensis ENSPCAG0000000583422 retrocopies
Pongo abelii ENSPPYG00000014675 10 retrocopies
Pteropus vampyrus ENSPVAG0000000091949 retrocopies
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
Sus scrofa ENSSSCG0000002519215 retrocopies
Tupaia belangeri ENSTBEG0000000604218 retrocopies
Tursiops truncatus ENSTTRG0000001428913 retrocopies
Vicugna pacos ENSVPAG000000020231 retrocopy



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