RetrogeneDB ID:

retro_ptro_2405

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:156274266..156275001(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C6orf203
Ensembl ID:ENSPTRG00000018464
Aliases:None
Description:chromosome 6 open reading frame 203 [Source:HGNC Symbol;Acc:17971]


Retrocopy-Parental alignment summary:






>retro_ptro_2405
GTTATAAGTGCCATGGCTATGACTAGTGTCAAATTGCATGCTGGTGTTTTAAGAAAGCCAGATACCTGGATTGGACTCTG
GGGTGTTCTCTGAGGAACACCTTCATCACACAAACTCTGTACTTCCTGGAATCAGTACTTGTATTTTTCTAGTACCAAGT
TACATGCACCAAATTATAAAACACTTTTCCATAACATTTTCTCACTGAGACTCCCGGGGCTTTTAATATCTCTGGAATAT
TTTTTTCCATTTTCCATAAGACTCAAAAGTAATATAAGCTCTACAAAATCTAGTAAAAAGTATCGGCAAAAAACAGGAGA
TGAGGAGGACTCTGATGCAGAAAGTGATCAGAACGAGATGAGTGAGCAGGAAGAGGAGCTTGAGGATGGCCTTACTATAG
CAAAGACTATCAAGACCTGGAAACAGTAGTGCGGTCTTTTCAGGATGACGTTGTCCTGAAGACAAGCCTGGATATTGGAA
GAAACAAAGTGGGAGATGCATTCTGCAAAGGTGAATTCAGGCTGAATGGGGAAAAATTATGGAAGAAAAGCAGAATGGTC
AAAGTGGGAGATACATTGGATCTTCTCATTGGAGAGGATAAGGAAGCAGGAACAGAGACAGTGATGCAGATTCTCCCAAA
AAAAAGTGTTTGAAGAGAAGACTGAAAGTGACAAATACACAGTGGTATTACAGCAGTGGGAAAACTTAAAAATGCCTAAG
AAGAGAATGTCTAAA

ORF - retro_ptro_2405 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.54 %
Parental protein coverage: 99.59 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalIISAMAMASVKLLAGVLRKPDAWIGLWGVLRGTPSSYKLCTSWNRYLYFSSTKLRAPNYKTLFYNIFSLR
.ISAMAM.SVKL.AGVLRKPD.WIGLWGVL.GTPSS.KLCTSWN.YLYFSSTKL.APNYKTLF.NIFSLR
RetrocopyVISAMAMTSVKLHAGVLRKPDTWIGLWGVL*GTPSSHKLCTSWNQYLYFSSTKLHAPNYKTLFHNIFSLR
ParentalLPGLLLSPECIFPFSVRLKSNIRSTKSTKKSLQKV-DEEDSDEESDHDEMSEQEEELEDDPTVV-KNYKD
LPGLL.S.E..FPFS.RLKSNI.STKS.KK..QK..DEEDSD.ESD..EMSEQEEELED..T...K.Y.D
RetrocopyLPGLLISLEYFFPFSIRLKSNISSTKSSKKYRQKTGDEEDSDAESDQNEMSEQEEELEDGLTIA<KDYQD
ParentalLEKAVQSFRYDVVLKTGLDIGRNKVEDAFYKGELRLNEEKLWKKSRTVKVGDTLDLLIGEDKEAGTETVM
LE..V.SF..DVVLKT.LDIGRNKV.DAF.KGE.RLN.EKLWKKSR.VKVGDTLDLLIGEDKEAGTETVM
RetrocopyLETVVRSFQDDVVLKTSLDIGRNKVGDAFCKGEFRLNGEKLWKKSRMVKVGDTLDLLIGEDKEAGTETVM
ParentalRIL-LKKVFEEKTESEKYRVVLRRWKSLKLPKKRMSK
.IL....VFEEKTES.KY.VVL..W..LK.PKKRMSK
RetrocopyQIL>XXXVFEEKTESDKYTVVLQQWENLKMPKKRMSK

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 .00 RPM 6 .43 RPM
SRP007412_cerebellum 0 .00 RPM 6 .52 RPM
SRP007412_heart 0 .03 RPM 10 .26 RPM
SRP007412_kidney 0 .00 RPM 10 .85 RPM
SRP007412_liver 0 .00 RPM 6 .45 RPM
SRP007412_testis 0 .00 RPM 7 .06 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2405 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2405 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2405 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3538
Gorilla gorilla retro_ggor_2389

Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000037321 retrocopy
Homo sapiens ENSG000001303491 retrocopy
Gorilla gorilla ENSGGOG000000061131 retrocopy
Macropus eugenii ENSMEUG000000135341 retrocopy
Microcebus murinus ENSMICG000000041371 retrocopy
Macaca mulatta ENSMMUG000000073911 retrocopy
Nomascus leucogenys ENSNLEG000000134502 retrocopies
Otolemur garnettii ENSOGAG000000088392 retrocopies
Pongo abelii ENSPPYG000000168851 retrocopy
Pan troglodytes ENSPTRG00000018464 2 retrocopies
retro_ptro_1453, retro_ptro_2405 ,
Tursiops truncatus ENSTTRG000000088372 retrocopies



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