RetrogeneDB ID:

retro_ptro_2454

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:88896501..88897549(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTB
Ensembl ID:ENSPTRG00000018890
Aliases:ACTB, beta-actin
Description:Pan troglodytes actin, beta (ACTB), mRNA. [Source:RefSeq mRNA;Acc:NM_001009945]


Retrocopy-Parental alignment summary:






>retro_ptro_2454
GCTCCCCAGGCCGTCTTCCCCTCCATTGTGGGGCACCCCAGGCACCAGGGAGTGATGGTGGGCATGGGTCAGAAGGACTC
CTATGTGGGCAAGGAGGCCCAGAGCAAGAGAGGCATCCTGACTCTGAAGTACCCCATCAAGCATGGCAACGTCACCAAAT
GGGACGACATGGAGAAGATCTGGCACCACACCTACAACGAGGTGCGTGTGACTGCTGAGGAGCACCCCGTGCTGCTGACT
GAGGCCCCCCTGAACCCCAAGCCCAACCATGAGAAGACGACCCAGTTCATCATGTTTGAGACCTTCAACACCCCAGCCAT
GTATGTGGCCATCCAGGCCGTGCTGTCCCTGTATGCCTCTGGCGGTACCACTGGCATCGTGATGCACCCCGGTGACAGGG
TCACCCACACTCTGTCCATCTAGGAGGGGTACGCCCTCCCCACGCCATCCTGCGTCTGGACCTGGCTGGCGGGGACCTGA
CTAACTACCTCAAGAAGACCCTCACCCAGCACAGCTACAGCTTCACCACCACGCTGAGCAGGAAATCATGTGTGACATCA
AGGAGAAGCTGTGCTACGTCGCCCTGGAATTCGAGCAGGAGATGGCCTCGGCGGCCTCCAGCTCCTCCCTGGAGAAGAGC
TATGAGCTGCCAGATGGCCAGGTCATCACCATCGGCAATGAGCGGTTCCGCTGCCCCAAGGCACTCTTCCAGCCTTCCTT
TCTGGGCATGGAATCCTGTGGCATCCATGACACTACCTTCAACTCCATTATGAAGTGTGACGTGGACAACCACAAAGACC
TGTACGCCAACACAGTGCTGTCTGGCGGCACCACCATGTACCCTGGCATCACAGACAGGATGCAGAAGGAGATCACCACC
CTGGCGCCCAGCACGATGAAGATCAAGATCATTGCTCCTCCCCAGTGCAAGCACTCCGTGTGGATTGGCTACTCCATCCT
GGCCTCCACGTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTAGGACGAGTCCGGCCCCTCCATCGTCCACCACA
AATGCTTC

ORF - retro_ptro_2454 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.4 %
Parental protein coverage: 93.33 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELR
AP.AVFPSIVG.PRHQGVMVGMGQKDSYVG.EAQSKRGILTLKYPI.HG.VT.WDDMEKIWHHT.YNE.R
RetrocopyAPQAVFPSIVGHPRHQGVMVGMGQKDSYVGKEAQSKRGILTLKYPIKHGNVTKWDDMEKIWHHT-YNEVR
ParentalVAPEEHPVLLTEAPLNPKANREKMTQ-IMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVP
V..EEHPVLLTEAPLNPK.N.EK.TQ.IMFETFNTPAMYVAIQAVLSLYASG.TTGIVM..GD.VTHT..
RetrocopyVTAEEHPVLLTEAPLNPKPNHEKTTQFIMFETFNTPAMYVAIQAVLSLYASGGTTGIVMHPGDRVTHTLS
ParentalIYEGYALP-HAILRLDLAGRDLTDYLMKILTERGYSFTTT-AEREIVRDIKEKLCYVALDFEQEMATAAS
I.EGYALP.HAILRLDLAG.DLT.YL.K.LT...YSFTTT.AE.EI..DIKEKLCYVAL.FEQEMA.AAS
RetrocopyI*EGYALP<HAILRLDLAGGDLTNYLKKTLTQHSYSFTTT<AEQEIMCDIKEKLCYVALEFEQEMASAAS
ParentalSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGG
SSSLEKSYELPDGQVITIGNERFRCP.ALFQPSFLGMESCGIH.TTFNSIMKCDVD..KDLYANTVLSGG
RetrocopySSSLEKSYELPDGQVITIGNERFRCPKALFQPSFLGMESCGIHDTTFNSIMKCDVDNHKDLYANTVLSGG
ParentalTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHR
TTMYPGI.DRMQKEIT.LAPSTMKIKIIAPP..K.SVWIG.SILAS.STFQQMWISKQE.DESGPSIVH.
RetrocopyTTMYPGITDRMQKEITTLAPSTMKIKIIAPPQCKHSVWIGYSILASTSTFQQMWISKQE*DESGPSIVHH
ParentalKCF
KCF
RetrocopyKCF

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 1976 .36 RPM
SRP007412_cerebellum 0 .07 RPM 1129 .84 RPM
SRP007412_heart 0 .00 RPM 382 .11 RPM
SRP007412_kidney 0 .05 RPM 1474 .96 RPM
SRP007412_liver 0 .07 RPM 1774 .09 RPM
SRP007412_testis 0 .21 RPM 315 .31 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_2454 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2454 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2454 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3631
Gorilla gorilla retro_ggor_2449
Pongo abelii retro_pabe_2978
Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000101471 retrocopy
retro_apla_2,
Canis familiaris ENSCAFG000000160203 retrocopies
retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus ENSCJAG000000000082 retrocopies
retro_cjac_243, retro_cjac_56,
Dipodomys ordii ENSDORG000000100791 retrocopy
retro_dord_11,
Equus caballus ENSECAG000000159352 retrocopies
retro_ecab_271, retro_ecab_994,
Felis catus ENSFCAG000000067881 retrocopy
retro_fcat_1613,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pan troglodytes ENSPTRG000000028941 retrocopy
retro_ptro_1567,
Pan troglodytes ENSPTRG00000018890 27 retrocopies
retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454 , retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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