RetrogeneDB ID:

retro_sscr_565

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:17:35507066..35507623(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
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_565
ATAAAGTGAATGGTGGTGGGAGATAGCGCTGTAGGTAAAACCTGCCTACCAATCAGTGCATTTCGTGGAGCATATATCCC
CACTGTCTTTGACAACTATTCTGCCAATATTATGATGGATGGAAAACCTGTGAATCTGGGCTTATGAGATATTGCAGGAC
AAGAAAATTATGACCAATTTACATCTCCTATCCTATCCGCAAATAGATGTAGTCTTAATTTGCTTTTCCGCTGGAAGTGC
TGCAGCATTTGAAAATGTTTGTGCAAAGTGGTATCCTGAAGTGCAACACCGTTATCCCAACACTCCTGTCATCCTGGTGG
GACGAAACTTGATGTCAGGGATGATAACGACACGACTGAGAAACCGAGGGAGAAGAAGCCGACTCTCATCACCTACCCAC
AGGGTTGGCCATGGCAAAGGAGATCTCTGTCGTAAAATACCTGGAGTGCTGGCTCATGCAGGCAGGCCTCGGGACGGTAA
CAGCGCTTGAGGAAACTATTCCAGTGGTTCTCTGCCTGCCTCCTATCAAGACGAGGAAGAGAAAATGCCTGCTGTTA

ORF - retro_sscr_565 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.95 %
Parental protein coverage: 98.44 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDSKPVNLGLWDTAGQEDYDR-LRPLSY
IK..VVGD.AVGKTCL.IS....AF.G.YIPTVFDNYSAN.M.D.KPVNLGL.D.AGQE.YD..L..LSY
RetrocopyIK*MVVGDSAVGKTCLPIS----AFRGAYIPTVFDNYSANIMMDGKPVNLGL*DIAGQENYDQ>LHLLSY
ParentalPQTDVFLICFSLVSPASYENVRAKWFPEVRHHCPSTPIILV-GTKLDLRDDKDTIEKLKEKKLAPITYPQ
PQ.DV.LICFS..S.A..ENV.AKW.PEV.H..P.TP.ILV.GTKLD.RDD.DT.EK..EKK...ITYPQ
RetrocopyPQIDVVLICFSAGSAAAFENVCAKWYPEVQHRYPNTPVILV<GTKLDVRDDNDTTEKPREKKPTLITYPQ
Parental-GLALAKEIDSVKYLECSALTQRGLKTV--FDEAIRAVLCPQPTRPQKRPCSIL
.GLA.AKEI..VKYLEC..L.Q.GL.TV....E.I..VLC..P....KR.C..L
Retrocopy<GLAMAKEISVVKYLEC-WLMQAGLGTVTALEETIPVVLCLPPIKTRKRKCLLL

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
SRP014902_placenta 0 .00 RPM 1 .33 RPM
SRP014902_testis 0 .00 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

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_565 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_565 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_565 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
retro_amel_1691, retro_amel_647,
Callithrix jacchus ENSCJAG000000021444 retrocopies
retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Equus caballus ENSECAG000000225702 retrocopies
retro_ecab_619, retro_ecab_705,
Erinaceus europaeus ENSEEUG000000095091 retrocopy
retro_eeur_20,
Felis catus ENSFCAG000000257762 retrocopies
retro_fcat_1064, retro_fcat_826,
Gorilla gorilla ENSGGOG000000106122 retrocopies
retro_ggor_1403, retro_ggor_188,
Loxodonta africana ENSLAFG000000130121 retrocopy
retro_lafr_117,
Macropus eugenii ENSMEUG000000122952 retrocopies
retro_meug_252, retro_meug_552,
Microcebus murinus ENSMICG000000177754 retrocopies
retro_mmur_1104, retro_mmur_1557, retro_mmur_20, retro_mmur_600,
Myotis lucifugus ENSMLUG000000126682 retrocopies
retro_mluc_326, retro_mluc_860,
Macaca mulatta ENSMMUG000000188542 retrocopies
retro_mmul_1346, retro_mmul_210,
Mustela putorius furoENSMPUG000000126822 retrocopies
retro_mputfur_872, retro_mputfur_911,
Nomascus leucogenys ENSNLEG000000147597 retrocopies
retro_nleu_1215, retro_nleu_1330, retro_nleu_2094, retro_nleu_2355, retro_nleu_689, retro_nleu_724, retro_nleu_87,
Oryctolagus cuniculus ENSOCUG000000161151 retrocopy
retro_ocun_43,
Otolemur garnettii ENSOGAG000000041381 retrocopy
retro_ogar_2977,
Pongo abelii ENSPPYG000000117913 retrocopies
retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pteropus vampyrus ENSPVAG000000022812 retrocopies
retro_pvam_21, retro_pvam_609,
Sarcophilus harrisii ENSSHAG000000148521 retrocopy
retro_shar_763,
Sus scrofa ENSSSCG000000035201 retrocopy
retro_sscr_899,
Sus scrofa ENSSSCG000000084391 retrocopy
retro_sscr_102,
Sus scrofa ENSSSCG00000021944 4 retrocopies
retro_sscr_40, retro_sscr_565 , retro_sscr_582, retro_sscr_882,
Ictidomys tridecemlineatus ENSSTOG000000237661 retrocopy
retro_itri_510,
Tursiops truncatus ENSTTRG000000010998 retrocopies
retro_ttru_1029, retro_ttru_1065, retro_ttru_1188, retro_ttru_1599, retro_ttru_1904, retro_ttru_318, retro_ttru_379, retro_ttru_825,


Copyright © RetrogeneDB 2014-2017