RetrogeneDB ID:

retro_ptro_1272

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:18:58544670..58545788(+)
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_1272
ATGGATGATGATACTGTCACCCTCGTCATCAACAATGGCTCTGGCATGTGCAGGGCTGGCTTCGCAGGCGACAATGCTCT
CCAGGCCATCTTCCTCTCCATCATGGGGCACCCCAGGCACCAGGGTGTGATGGTGGGCATGGGTCAGAAGGACTCCTACG
TGGGCAACAAGGGCCCAGAGCAAGAGAGGCATTCTGACCCTGAAGTACTGCATCGAGCATGGCATCGTCACCAACTGGGA
GGACATGGAGGAGATTTGGCTCCACACTTTCTACAGTGAGCTGCATGTGGCTCCTGAGGAGCACCCCCTGCTGCTGACCG
AGGCCTCTCTGAACCCCAAGGCCAACCACAAGAAGGTAAACCAGATCATGTTTGAGACCTTCAACACCCCAGCCATGTAT
GTGGCCATCCAGGCCTTGCTGTCCCTGTAAGCCTCTGGCCATACCACTGGCATCGTGATGGACTCTGGTGATGGGGTCAC
CCACACTGTGCCCATCTACGGGGGGGTATGCCCTCCCCCACACCATCCTGCATCTGGACCTGGCTGGCCCAGACCTGACT
GACCACCTCATGAAGATCCTCACCGAGCGCGGCTACAGCTTCACCACCACGGCCAAGCGGGAAATCGTGCATGACATCAA
GGAGAAGCTGTGCTATGTCGCCCTGGACTTTGAGCAGGAGATGGCCATGGTGGCCTCCAACCCCCTGCTGGAGAAGAGCT
AGGAGCTGCCAGGTGGCCAAGTCATCTGCAACGAGCAGTTCCGCTGCCCTGAGGCACTCTTTCAGCCTTCCTTCCTGGGC
ATGGAATCCTGTGGCATCCATGAAACTACCTTCAACTCCATCATGAAGTGTGACATGGACATCTGCAAAGACCGGTACGT
CAACACAGTGCTGTCTGGCGGCACCACCTTGTACCCTGGCATCGCCGACAAGATGCAGGAGATCAGCGGCCTGGCTCCAA
GCACGATGAAGATCAAGATCGTTGCTCCTTCTGAGCGCAAATACTCCATGTGGATTGGCAGCTCCATCCTGGCCTCGCTG
TCCACCTCCCAGCAGATATGGATCAGCAAGCAGGAGTATGACGAGTCCAGCCCCTCCATCGTCCACCACAAATGCTTC

ORF - retro_ptro_1272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.23 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDE-AQSKRGILTLKY
MDDD...LV..NGSGMC.AGFAGD.A..A.F.SI.G.PRHQGVMVGMGQKDSYVG...AQSKRGILTLKY
RetrocopyMDDDTVTLVINNGSGMCRAGFAGDNALQAIFLSIMGHPRHQGVMVGMGQKDSYVGNK>AQSKRGILTLKY
ParentalPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAV
.IEHGIVTNW.DME.IW.HTFY.EL.VAPEEHP.LLTEA.LNPKAN..K..QIMFETFNTPAMYVAIQA.
RetrocopyCIEHGIVTNWEDMEEIWLHTFYSELHVAPEEHPLLLTEASLNPKANHKKVNQIMFETFNTPAMYVAIQAL
ParentalLSLYASGRTTGIVMDSGDGVTHTVPIY-EGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI
LSL.ASG.TTGIVMDSGDGVTHTVPIY..GYALPH.IL.LDLAG.DLTD.LMKILTERGYSFTTTA.REI
RetrocopyLSL*ASGHTTGIVMDSGDGVTHTVPIY>GGYALPHTILHLDLAGPDLTDHLMKILTERGYSFTTTAKREI
ParentalVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETT
V.DIKEKLCYVALDFEQEMA..AS...LEKS.ELP.GQVI...NE.FRCPEALFQPSFLGMESCGIHETT
RetrocopyVHDIKEKLCYVALDFEQEMAMVASNPLLEKS*ELPGGQVIC--NEQFRCPEALFQPSFLGMESCGIHETT
ParentalFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
FNSIMKCD.DI.KD.Y.NTVLSGGTT.YPGIAD.MQ.EI..LAPSTMKIKI.AP.ERKYS.WIG.SILAS
RetrocopyFNSIMKCDMDICKDRYVNTVLSGGTTLYPGIADKMQ-EISGLAPSTMKIKIVAPSERKYSMWIGSSILAS
ParentalLSTFQQMWISKQEYDESGPSIVHRKCF
LST.QQ.WISKQEYDES.PSIVH.KCF
RetrocopyLSTSQQIWISKQEYDESSPSIVHHKCF

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 .00 RPM 1129 .84 RPM
SRP007412_heart 0 .00 RPM 382 .11 RPM
SRP007412_kidney 0 .00 RPM 1474 .96 RPM
SRP007412_liver 0 .20 RPM 1774 .09 RPM
SRP007412_testis 0 .00 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_1272 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1272 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1272 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1894
Gorilla gorilla retro_ggor_1387
Pongo abelii retro_pabe_1575
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,


Copyright © RetrogeneDB 2014-2017