RetrogeneDB ID:

retro_pabe_2308

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:57895938..57896837(-)
Located in intron of:ENSPPYG00000013649
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTG1
Ensembl ID:ENSPPYG00000008735
Aliases:None
Description:actin, gamma 1 [Source:HGNC Symbol;Acc:144]


Retrocopy-Parental alignment summary:






>retro_pabe_2308
CCCATTGAGCACAGCATCGTCATCAACTGGGATGACATGAAGAAGATTTGGCACCACACCTACGATGAGCTGCGTGTGGC
CCCGGAGGAGCACCTGGTGCTGCTGACAGAGGCCCTTGTGAACCCCAAGGCCAACAGAGAGAAGATGACCCAGATCATGT
TTGAGACCTTCAACACCCTGTCCATGTACGTGGCCATCCAGGCCATGCTGTCCCTCTACACCTCTGGATGCACCACTGGC
ATTGTTATGGACCCTGGAGATGGGGTCACTCATATAGCGCCCATCTATGAGGCCTAAGCCCTCCCCCATGCCATCCTGTG
TCTGGACCTGGCTGGTGGGGACCTGACTGACTACCTCATGAAGATCCTCACCAAGCGCAGCTACAGCTTCAACACCGTGG
CTGAGTGGAGATCATGGGCGACATCAAGGAGAAGCCATGCTATGTTGCCCTGGACTTTGAACAGGAGATGGCCACCGCCG
CATCCTCCTCCTCCTCCTCCCTGGAGAAGAGCTAGGAGCTGCCCGACAGCCTGGTCATCACCGTTAGCAACGAGTGGTCC
TGGTGTCTGGAGGCGCTGTTATAGCCTTCCTTCCTAGGCATGGAATCTTGTGGCATCCATTAGACCACCTTCAACTCCAT
CATGAAGTGTGATGTGGACATCTGCAAAGACCTGCATGCCAACAAGGTGCTGTCTAGCGGCACCACCATGTACCCGGGCA
TCACCAACAGGATGCAGAAGGCAATCACTGCCCTGGCACCCAGCACCATGAAGATCAAGATCATTGTGCCCCCAGAGCAC
AAGTACTCTGTGTGGATCCGCAGCTCCATCCTGGCCTCACTGTCCACCTTCCAGCAGATGTGGATTAGCAAGCAGGAGTA
CAAGTTGGCCCCTCCATCG

ORF - retro_pabe_2308 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.14 %
Parental protein coverage: 79.73 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAV
PIEH.IV.NWDDM.KIWHHT.Y.ELRVAPEEH.VLLTEA..NPKANREKMTQIMFETFNT..MYVAIQA.
RetrocopyPIEHSIVINWDDMKKIWHHT-YDELRVAPEEHLVLLTEALVNPKANREKMTQIMFETFNTLSMYVAIQAM
ParentalLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAER-EI
LSLY.SG.TTGIVMD.GDGVTH..PIYE..ALPHAIL.LDLAG.DLTDYLMKILT.R.YSF.T.AE..EI
RetrocopyLSLYTSGCTTGIVMDPGDGVTHIAPIYEA*ALPHAILCLDLAGGDLTDYLMKILTKRSYSFNTVAEW<EI
ParentalVRDIKEKLCYVALDFEQEMATAASSSSL--EKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHE
..DIKEK.CYVALDFEQEMATAA.......EKS.ELPD..VIT..NE...C.EAL..PSFLGMESCGIH.
RetrocopyMGDIKEKPCYVALDFEQEMATAAXXXXXXXEKS*ELPDSLVITVSNEWSWCLEALL*PSFLGMESCGIH*
ParentalTTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSIL
TTFNSIMKCDVDI.KDL.AN.VLS.GTTMYPGI..RMQK.ITALAPSTMKIKII.PPE.KYSVWI..SIL
RetrocopyTTFNSIMKCDVDICKDLHANKVLSSGTTMYPGITNRMQKAITALAPSTMKIKIIVPPEHKYSVWIRSSIL
ParentalASLSTFQQMWISKQEYDESGPS
ASLSTFQQMWISKQEY....PS
RetrocopyASLSTFQQMWISKQEYKLAPPS

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 .11 RPM 426 .62 RPM
SRP007412_cerebellum 0 .36 RPM 117 .22 RPM
SRP007412_heart 0 .00 RPM 145 .94 RPM
SRP007412_kidney 0 .00 RPM 354 .54 RPM
SRP007412_liver 0 .03 RPM 440 .45 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2308 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2308 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2308 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2605
Pan troglodytes retro_ptro_1756
Gorilla gorilla retro_ggor_1825

Parental genes homology:
Parental genes homology involve 25 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
Callithrix jacchus ENSCJAG000000028853 retrocopies
Cavia porcellus ENSCPOG000000121011 retrocopy
Equus caballus ENSECAG000000186001 retrocopy
Felis catus ENSFCAG000000264342 retrocopies
Homo sapiens ENSG0000018400910 retrocopies
Gallus gallus ENSGALG000000287491 retrocopy
Gorilla gorilla ENSGGOG000000140436 retrocopies
Loxodonta africana ENSLAFG000000091671 retrocopy
Monodelphis domestica ENSMODG000000026473 retrocopies
Mustela putorius furoENSMPUG000000116101 retrocopy
Mus musculus ENSMUSG000000628257 retrocopies
Nomascus leucogenys ENSNLEG000000155063 retrocopies
Petromyzon marinus ENSPMAG000000041611 retrocopy
Pongo abelii ENSPPYG000000024591 retrocopy
Pongo abelii ENSPPYG000000026051 retrocopy
Pongo abelii ENSPPYG000000063181 retrocopy
Pongo abelii ENSPPYG00000008735 11 retrocopies
Pongo abelii ENSPPYG0000001733623 retrocopies
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
Rattus norvegicus ENSRNOG000000367011 retrocopy
Sus scrofa ENSSSCG000000283551 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
Xenopus tropicalis ENSXETG000000251161 retrocopy



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