RetrogeneDB ID:

retro_pabe_1816

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:20:27232828..27233408(-)
Located in intron of:ENSPPYG00000010859
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTB
Ensembl ID:ENSPPYG00000017336
Aliases:None
Description:Actin, cytoplasmic 1 Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:Q5R6G0]


Retrocopy-Parental alignment summary:






>retro_pabe_1816
GGCCGGCCAGGACCTGACCACCTCATGAAGATTCTCACAGAATATGACTACAGCTTCCCTACCACGGCCAAGTGGGAGAT
CGTGCGTGACATCAAGGAGAGGCAGTGCTACGTTGCCCTGGACTTTGAGCAGGAGATGGCCACCACTACGTCATCCTTCT
CCCTGGAGAAAAGCTACAAACTACCTGACAGCCAGGTGATCACCATTGGCAACATGCAGTTCCAGTGTTTGGAGGCGTTG
TTCCAGCCCTTCTTTCTGGGTGTGGAATTTTGCAGCATCCATGTGGAATTTTGCAGCTCCATCATAAGGTGTGATGTGGA
CATCCACAAGGACCTGTATGCCAACACGATGCTGGCCAGTGGCACCACCATGTACCCAAGCATCTCCAGCAGGATGCAGA
AAGAGATCACTGCCCTGGTGCCAGCACAAGTAAGATCAAGATCATCGTGCTCCCAGAGCACAAGTACTCCGTGTGGATCA
GCAGCTCCATCCTGGCCTCGTTGTCCACTTTCCAGCAGATGTGGATTAGCAAGCAGGAATATGACAAGTCGGGCCCCTCC
ATGTCCACCGCAAATGCTTC

ORF - retro_pabe_1816 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.43 %
Parental protein coverage: 51.73 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIG
GR...D.LMKILTE..YSF.TTA..EIVRDIKE..CYVALDFEQEMAT..SS.SLEKSY.LPD.QVITIG
RetrocopyGRPGPDHLMKILTEYDYSFPTTAKWEIVRDIKERQCYVALDFEQEMATTTSSFSLEKSYKLPDSQVITIG
ParentalNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALA
N..F.C.EALFQP.FL.................CDVDI.KDLYANT.L..GTTMYP.I..RMQKEITAL.
RetrocopyNMQFQCLEALFQPFFLXXXXXXXXXXXXXXXIRCDVDIHKDLYANTMLASGTTMYPSISSRMQKEITALV
ParentalP-STMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSI-VHRKCF
P.ST.KIKII..PE.KYSVWI..SILASLSTFQQMWISKQEYD.SGPS..VHRKCF
RetrocopyP<STSKIKIIVLPEHKYSVWISSSILASLSTFQQMWISKQEYDKSGPSM<VHRKCF

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 .17 RPM 1655 .73 RPM
SRP007412_cerebellum 0 .00 RPM 578 .33 RPM
SRP007412_heart 0 .03 RPM 386 .86 RPM
SRP007412_kidney 0 .10 RPM 1247 .35 RPM
SRP007412_liver 0 .15 RPM 1654 .82 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1816 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1816 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1816 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2405
Gorilla gorilla retro_ggor_1495

Parental genes homology:
Parental genes homology involve 24 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
Cavia porcellus ENSCPOG000000134671 retrocopy
Homo sapiens ENSG000000756246 retrocopies
Gallus gallus ENSGALG000000096211 retrocopy
Gorilla gorilla ENSGGOG0000000113318 retrocopies
Loxodonta africana ENSLAFG000000091671 retrocopy
Meleagris gallopavo ENSMGAG000000039602 retrocopies
Macaca mulatta ENSMMUG000000111531 retrocopy
Mustela putorius furoENSMPUG000000166122 retrocopies
Mus musculus ENSMUSG000000295807 retrocopies
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
Otolemur garnettii ENSOGAG000000083481 retrocopy
Petromyzon marinus ENSPMAG000000041611 retrocopy
Pongo abelii ENSPPYG000000024591 retrocopy
Pongo abelii ENSPPYG000000026051 retrocopy
Pongo abelii ENSPPYG000000063181 retrocopy
Pongo abelii ENSPPYG0000000873511 retrocopies
Pongo abelii ENSPPYG00000017336 23 retrocopies
Rattus norvegicus ENSRNOG0000003425410 retrocopies
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
Sus scrofa ENSSSCG000000075851 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
Xenopus tropicalis ENSXETG000000251161 retrocopy



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