RetrogeneDB ID:

retro_pabe_2546

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:111936045..111936610(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAC3
Ensembl ID:ENSPPYG00000008763
Aliases:None
Description:ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Source:HGNC Symbol;Acc:9803]


Retrocopy-Parental alignment summary:






>retro_pabe_2546
ATGCAGGCCATCAAGGGTGTGGTGGTGGGAGACGGAGCTGTAGGTGAAATTTGCCTACTGATCAGTTACGCAACCAATGC
ATTTCCTGGAGAATATATCCCTACTGTCTTTGACAATTATTCTGCCAATGTTTTGGTAGATGGAAAACCGGTGAATCTGG
GCTTATGGGATACAGTTGCTCAAGAAGATTATGACAGATTATGCCGCCTATCCTATCCGCAAACAGATATGTTCTTAATT
TGCTTTTCCCTTGTGAGTCCTGCATCATTTGAAAGTGTCAGTGCAAAGTGGTATCCTGAGGTGCGGCACCACTGTCCCAA
CACTCCCATCATCCTATTGGGAACTAAACTTGAACTTAGGGATGATAAAGACACGATCGAGAAACTGAAGGAGAAGAAGC
TGACTCCCATCACCTATCTGCAGGGTCTAGCCATGGCTAAGGAGATTGGTGCTGTAAAATACCTGAAGTGCTCGGCACTC
ACACAGCAAGTCCTCAACAGTGTTTGACAAAGAGATCTAAGCAGTCCTCTGCCCACCTCCCTTGAAGAAGAGGAAGAGAA
AATGC

ORF - retro_pabe_2546 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.84 %
Parental protein coverage: 98.44 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalIQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
.QAIK.VVVGDGAVG..CLLISY.TNAFPGEYIPTVFDNYSANV.VDGKPVNLGLWDT..QEDYDRL..L
RetrocopyMQAIKGVVVGDGAVGEICLLISYATNAFPGEYIPTVFDNYSANVLVDGKPVNLGLWDTVAQEDYDRLCRL
ParentalSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPQTPILLVGTKLDLRDDKDTIERLRDKKLAPITYP
SYPQTD.FLICFSLVSPASFE.V.AKWYPEVRHHCP.TPI.L.GTKL.LRDDKDTIE.L..KKL.PITY.
RetrocopySYPQTDMFLICFSLVSPASFESVSAKWYPEVRHHCPNTPIILLGTKLELRDDKDTIEKLKEKKLTPITYL
ParentalQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVL-CPPPVKKPGKKC
QGLAMA.EIG.VKYL.CSALTQ..L..V........L..PP..KK...KC
RetrocopyQGLAMAKEIGAVKYLKCSALTQQVLNSV*QRDLSSPL>PPP-LKKRKRKC

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 13 .16 RPM
SRP007412_cerebellum 0 .00 RPM 8 .51 RPM
SRP007412_heart 0 .03 RPM 0 .24 RPM
SRP007412_kidney 0 .10 RPM 7 .06 RPM
SRP007412_liver 0 .09 RPM 1 .38 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2546 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2546 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2546 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3072
Gorilla gorilla retro_ggor_2110
Macaca mulatta retro_mmul_1964

Parental genes homology:
Parental genes homology involve 13 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173641 retrocopy
Callithrix jacchus ENSCJAG000000181941 retrocopy
Cavia porcellus ENSCPOG000000138611 retrocopy
Echinops telfairi ENSETEG000000129023 retrocopies
Macropus eugenii ENSMEUG000000061961 retrocopy
Otolemur garnettii ENSOGAG000000124671 retrocopy
Procavia capensis ENSPCAG000000099491 retrocopy
Pongo abelii ENSPPYG000000017556 retrocopies
Pongo abelii ENSPPYG00000008763 2 retrocopies
retro_pabe_1047, retro_pabe_2546 ,
Pongo abelii ENSPPYG000000117913 retrocopies
Pongo abelii ENSPPYG000000124392 retrocopies
Tupaia belangeri ENSTBEG000000072724 retrocopies
Takifugu rubripes ENSTRUG000000162011 retrocopy



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