RetrogeneDB ID:

retro_ptro_2337

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:30815227..30816519(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUCLA2
Ensembl ID:ENSPTRG00000005859
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2337
CGGACCACACTGCGGGCTGCTGCTCAGGTTCTGGGAAGTTCTGGATTGTTTAATAACCGTGGACTCCAAGTACAGCAGCA
ACAGCAAAGGAATCTCTCACTACATGAATACATGAGTATGGAATTATTGCAAGAAACTGGTGTCTCTGTTCCCAAAGGAT
ATGTGGCAAAGTGACCAGATGAAGCTTATGCAATTGCCAAAAAATTAGGTTCAAAAGATGTTGTGATGAAGGCACAGGTT
TTAGCTGGTGGTAGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGGAGGGGTGAAGATGGTTTTCTCTCCAGAAGAAGC
AAAAGCTGTTCCTTCACAAATGATTAGGAAACAGTTGTTTACCAAGCAAATGAGAGAAAAGGGCAGAATATGCAATCAGG
TATTGGTCTGTGAGTGAAAATATCCCAAGAGAGAGTGCTACTTTGCAAAAACAATGGAAAGGTCATTTCAAGGTCTTGTA
TTAATAGGAAGTTTACATAGTGGGGCCAACATTGAAGATGTTGCTGCTGAGACTCCTGAAGCAATAATTAAAGTACCTAT
TGATATTGTAGAAGGTATCAAAGAGGAATAAGCTCTCCAGCTTGCACAGAAGATGGGATTTCCATCTAATATTGTGGCTT
CAGCAGCAGAAAACATGATCAAGCTTTACAGCCTTTTTCTGAAATACGATGCAACCGTGATAGAAATAAATTCAATGGTG
GAAGATTCAGATGGAGCTGTATTGTGTATGGATGCAAAGATCAATTTTGACTCTAATTCAGCCTATCGCCAAAAGAAAAT
CTTTGATCTACAGGACTGGACCCAGGAAGATGAAAGGAACAAAGATGCTGCTAAGGCAGATCTCAACTACACTGGCCTCG
ATGGAAGTATAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTATGGCCACAATGGATATAATAAAACTTCATGGAGAGACT
CCAGCTAACTTCCTTGATGCTGGTGGTGGTGCTACAGTCCATCAAGTAACAGAAGCATTTAAGCCTATCACTTCAGCTAA
AAAGGTACTGGCTATTCTAGTCAACATTTGTGGAGGAATCATGCACTGTGATATTACAGCAAAGGGTATAGTCACGGCAG
TAAAAGGTTTGGAAATTAAGATACCTGTTGTGGTACAGTTACAAGTACACAAGTTGATGATGTTAAGGCACTAAAAGCAG
ACAGTGGACTTAAAATACTTGCTTGTGATGATTTGGTGGAAGCTGCTAGAGTGCTTGTAAAGCTCTCTGAAATAGTGAAG
CGAAGCAAGCGC

ORF - retro_ptro_2337 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.81 %
Parental protein coverage: 93.09 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalRTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSVPKGYVAKSPDEAYAIAKKLG
RT..RAAAQVLGSSGLFNN.GLQVQQQQQRNLSLHEYMSMELLQE.GVSVPKGYVAK.PDEAYAIAKKLG
RetrocopyRTTLRAAAQVLGSSGLFNNRGLQVQQQQQRNLSLHEYMSMELLQETGVSVPKGYVAK*PDEAYAIAKKLG
ParentalSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERK
SKDVV.KAQVLAGGRGKGTFESGLKGGVK.VFSPEEAKAV.SQMI.K.LFTKQ..EKGRICNQVLVCE.K
RetrocopySKDVVMKAQVLAGGRGKGTFESGLKGGVKMVFSPEEAKAVPSQMIRKQLFTKQMREKGRICNQVLVCE*K
ParentalYPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALQLAQKMGFPPN
YP.RE.YFA.TMERSFQG.VLIGS.H.G.NIEDVAAETPEAIIK.PIDI.EGIK.E.ALQLAQKMGFP.N
RetrocopyYPKRECYFAKTMERSFQGLVLIGSLHSGANIEDVAAETPEAIIKVPIDIVEGIKEE*ALQLAQKMGFPSN
ParentalIVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERD
IV.SAAENM.KLYSLFLKYDAT.IEIN.MVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDER.
RetrocopyIVASAAENMIKLYSLFLKYDATVIEINSMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERN
ParentalKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITSDKKVL
KDAAKA.LNY.GLDG.IGCLVNGAGLAMATMDIIKLHG.TPANFLD.GGGATVHQVTEAFK.ITS.KKVL
RetrocopyKDAAKADLNYTGLDGSIGCLVNGAGLAMATMDIIKLHGETPANFLDAGGGATVHQVTEAFKPITSAKKVL
ParentalAILVNIFGGIMRCDVIAQGIVMAVKDLEIKIPVVVRLQ-GTRVDDAKALIADSGLKILACDDLDEAARMV
AILVNI.GGIM.CD..A.GIV.AVK.LEIKIPVVV.LQ..T.VDD.KAL.ADSGLKILACDDL.EAAR..
RetrocopyAILVNICGGIMHCDITAKGIVTAVKGLEIKIPVVVQLQ<STQVDDVKALKADSGLKILACDDLVEAARVL
ParentalVKLSEIVTLAKQ
VKLSEIV...K.
RetrocopyVKLSEIVKRSKR

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 .23 RPM 52 .16 RPM
SRP007412_cerebellum 0 .14 RPM 40 .80 RPM
SRP007412_heart 0 .12 RPM 90 .79 RPM
SRP007412_kidney 0 .08 RPM 56 .54 RPM
SRP007412_liver 0 .00 RPM 8 .67 RPM
SRP007412_testis 0 .00 RPM 19 .81 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_2337 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2337 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2337 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3445
Gorilla gorilla retro_ggor_2327
Pongo abelii retro_pabe_2852
Parental genes homology:
Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146102 retrocopies
retro_acar_26, retro_acar_52,
Callithrix jacchus ENSCJAG000000092782 retrocopies
retro_cjac_1233, retro_cjac_2379,
Cavia porcellus ENSCPOG000000149611 retrocopy
retro_cpor_1113,
Homo sapiens ENSG000001361433 retrocopies
retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla ENSGGOG000000082243 retrocopies
retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta ENSMMUG000000075391 retrocopy
retro_mmul_1231,
Mustela putorius furoENSMPUG000000014881 retrocopy
retro_mputfur_768,
Nomascus leucogenys ENSNLEG000000029483 retrocopies
retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii ENSOGAG000000074521 retrocopy
retro_ogar_2196,
Pongo abelii ENSPPYG000000053522 retrocopies
retro_pabe_1939, retro_pabe_2852,
Pan troglodytes ENSPTRG00000005859 3 retrocopies
retro_ptro_1581, retro_ptro_1615, retro_ptro_2337 ,


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