RetrogeneDB ID:

retro_sscr_40

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:GL896504.1:7608..8184(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000022917
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RAC2
Ensembl ID:ENSSSCG00000021944
Aliases:None
Description:ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Source:HGNC Symbol;Acc:9802]


Retrocopy-Parental alignment summary:






>retro_sscr_40
ATGCAGACGATCAAATGTGTGGTTGTGGGGGATGGGGCTGTAGGTAAGACCTGTCTCCTCATCAGTTACACCACAAATGC
CTTTCCTGAGGAGTATATCCCCACTGTGTTTGACAACTATAGTGCCCAGACATCGGTGGATGGCCAAATCGTCAGCCTGA
ATCTGTGGGACACAGCTGGCCAAGAGGAGTATGACCGACTGCGAACGCTGTCCTACCCCCAGACTAATATCTTTGTCATT
TGTTTTTCCATTGGCAACCCATCCTCTTATGCCAACGTGAGGCATAAGTGGTACCCAGAGGTCTCGCATCATTGCCCCAA
TGTACCCGTTTTGCTGGTAGGCACCAAGAGGGACCTGCGGAGTGACCTTGAGACAGTGAAGAAGCTGAAGGAACAGAGCC
TAGTGCCCACAACTCCTCAGCAAGGCACTTCCCTGGCTAAGCAGGTGGGGGCTGTGAAGTATCTGGAATGTTCGGCCCTG
ATGCAGGATGGGGTCCATGAGGTATTTTCAGAAGCTGTCCGGGCTGTGCTTTACCCTGCCACAAAGAAGAACACCAAGAA
GTGTGTCCTCTTATAG

ORF - retro_sscr_40 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.19 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDSKPVNLGLWDTAGQEDYDRLRPL
MQ.IKCVVVGDGAVGKTCLLISYTTNAFP.EYIPTVFDNYSA...VD...V.L.LWDTAGQE.YDRLR.L
RetrocopyMQTIKCVVVGDGAVGKTCLLISYTTNAFPEEYIPTVFDNYSAQTSVDGQIVSLNLWDTAGQEEYDRLRTL
ParentalSYPQTDVFLICFSLVSPASYENVRAKWFPEVRHHCPSTPIILVGTKLDLRDDKDTIEKLKEKKLAPITYP
SYPQT..F.ICFS...P.SY.NVR.KW.PEV.HHCP..P..LVGTK.DLR.D..T..KLKE..L.P.T..
RetrocopySYPQTNIFVICFSIGNPSSYANVRHKWYPEVSHHCPNVPVLLVGTKRDLRSDLETVKKLKEQSLVPTTPQ
ParentalQGLALAKEIDSVKYLECSALTQRGLKTVFDEAIRAVLCPQPTRPQKRPCSIL
QG..LAK....VKYLECSAL.Q.G...VF.EA.RAVL.P..T......C..L
RetrocopyQGTSLAKQVGAVKYLECSALMQDGVHEVFSEAVRAVLYP-ATKKNTKKCVLL

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
SRP014902_placenta 0 .00 RPM 1 .33 RPM
SRP014902_testis 0 .14 RPM 17 .54 RPM
SRP018288_heart 0 .00 RPM 6 .31 RPM
SRP018288_kidney 0 .00 RPM 10 .64 RPM
SRP018288_liver 0 .00 RPM 11 .03 RPM
SRP018288_lung 0 .00 RPM 156 .61 RPM
SRP018856_adipose 0 .00 RPM 17 .25 RPM
SRP035408_brain 0 .00 RPM 1 .30 RPM
SRP035408_liver 0 .00 RPM 4 .70 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_40 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_40 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_40 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098892 retrocopies
Callithrix jacchus ENSCJAG000000021444 retrocopies
Equus caballus ENSECAG000000225702 retrocopies
Erinaceus europaeus ENSEEUG000000095091 retrocopy
Felis catus ENSFCAG000000257762 retrocopies
Gorilla gorilla ENSGGOG000000106122 retrocopies
Loxodonta africana ENSLAFG000000130121 retrocopy
Macropus eugenii ENSMEUG000000122952 retrocopies
Microcebus murinus ENSMICG000000177754 retrocopies
Myotis lucifugus ENSMLUG000000126682 retrocopies
Macaca mulatta ENSMMUG000000188542 retrocopies
Mustela putorius furoENSMPUG000000126822 retrocopies
Nomascus leucogenys ENSNLEG000000147597 retrocopies
Oryctolagus cuniculus ENSOCUG000000161151 retrocopy
Otolemur garnettii ENSOGAG000000041381 retrocopy
Pongo abelii ENSPPYG000000117913 retrocopies
Pteropus vampyrus ENSPVAG000000022812 retrocopies
Sarcophilus harrisii ENSSHAG000000148521 retrocopy
Sus scrofa ENSSSCG000000035201 retrocopy
Sus scrofa ENSSSCG000000084391 retrocopy
Sus scrofa ENSSSCG00000021944 4 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000237661 retrocopy
Tursiops truncatus ENSTTRG000000010998 retrocopies



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