RetrogeneDB ID:

retro_sscr_909

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:7:81934454..81934948(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSSCG00000030014
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sscr_909
TCTGTGCCATTTGTTCAAGGAATTCTTGTTGCAAAATATGATCCTATGATAGAAGATTCTTATAGAAAGCAAGTTGAAGT
AGGTACACAATAGCGTATGCTTGAAATCTTGCCTACTGCAGGAATGGAACAATTTTCAGCAATGAGGGACTTGTACATGA
AAAATGGAGAGGTTTTTCAGTAGTTTATTCCATCGCAACTCAGGCCATGTTTAGTGATTTATAAGATCCGAGAGAACAGA
TTCTTCGAGTTAAAGACACTGACGATGTTCCAATGATCCTGGTTGGTAATAAGTGTGACTTGGAAGATGAAAGAGTTGTA
GGAAAGGAATGAGGTCAAAATCTAGCAAGACAGTGGAACTACTGTGCCTTCTTAGAATCCTCTGCAAAATCAAAAAGAAG
TGTTAATGAGATCTTTTATGACTTAGTGCAACAAATTAACAGAAAAACTCTGGTGCCTGGGAAGACCTTCAAAAAGTCAT
CATATCAACTGCTT

ORF - retro_sscr_909 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.72 %
Parental protein coverage: 89.67 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQ-GFALVYSITAQS
.V.FVQGI.V.KYDP.IEDSYRKQVEV..Q..MLEIL.TAG.EQF.AMRDLYMKNG..GF..VYSI..Q.
RetrocopySVPFVQGILVAKYDPMIEDSYRKQVEVGTQ*RMLEILPTAGMEQFSAMRDLYMKNGE<GFSVVYSIATQA
ParentalTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIF
.F.DL.D.REQILRVKDTDDVPMILVGNKCDLEDERVVGKE.GQNLARQWN.CAFLESSAKSK..VNEIF
RetrocopyMFSDL*DPREQILRVKDTDDVPMILVGNKCDLEDERVVGKE*GQNLARQWNYCAFLESSAKSKRSVNEIF
ParentalYDLVRQINRKTPVPGKARKKSSCQLL
YDLV.QINRKT.VPGK..KKSS.QLL
RetrocopyYDLVQQINRKTLVPGKTFKKSSYQLL

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 23 .76 RPM
SRP014902_testis 0 .00 RPM 17 .40 RPM
SRP018288_heart 0 .00 RPM 10 .84 RPM
SRP018288_kidney 0 .00 RPM 14 .48 RPM
SRP018288_liver 0 .00 RPM 8 .80 RPM
SRP018288_lung 0 .00 RPM 22 .30 RPM
SRP018856_adipose 0 .00 RPM 6 .11 RPM
SRP035408_brain 0 .00 RPM 9 .66 RPM
SRP035408_liver 0 .00 RPM 13 .97 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_909 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_909 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_909 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 32 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086371 retrocopy
retro_amel_103,
Bos taurus ENSBTAG000000089673 retrocopies
retro_btau_1564, retro_btau_297, retro_btau_684,
Callithrix jacchus ENSCJAG000000072613 retrocopies
retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus ENSCPOG000000082724 retrocopies
retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus ENSDNOG0000001972418 retrocopies
retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Dipodomys ordii ENSDORG000000010861 retrocopy
retro_dord_521,
Erinaceus europaeus ENSEEUG000000100521 retrocopy
retro_eeur_327,
Echinops telfairi ENSETEG000000002421 retrocopy
retro_etel_11,
Homo sapiens ENSG000001273142 retrocopies
retro_hsap_3338, retro_hsap_4234,
Gorilla gorilla ENSGGOG000000256491 retrocopy
retro_ggor_2836,
Loxodonta africana ENSLAFG000000164601 retrocopy
retro_lafr_482,
Microcebus murinus ENSMICG000000131481 retrocopy
retro_mmur_116,
Myotis lucifugus ENSMLUG000000166062 retrocopies
retro_mluc_1126, retro_mluc_2211,
Macaca mulatta ENSMMUG000000114422 retrocopies
retro_mmul_1151, retro_mmul_1863,
Monodelphis domestica ENSMODG000000073235 retrocopies
retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Mus musculus ENSMUSG000000526811 retrocopy
retro_mmus_1370,
Nomascus leucogenys ENSNLEG000000035732 retrocopies
retro_nleu_1034, retro_nleu_481,
Oryctolagus cuniculus ENSOCUG000000295525 retrocopies
retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii ENSOGAG000000057462 retrocopies
retro_ogar_2260, retro_ogar_272,
Procavia capensis ENSPCAG000000109771 retrocopy
retro_pcap_8,
Pongo abelii ENSPPYG000000047511 retrocopy
retro_pabe_3403,
Pan troglodytes ENSPTRG000000051973 retrocopies
retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus ENSRNOG000000070484 retrocopies
retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sarcophilus harrisii ENSSHAG000000114971 retrocopy
retro_shar_425,
Sus scrofa ENSSSCG000000067531 retrocopy
retro_sscr_520,
Sus scrofa ENSSSCG000000211481 retrocopy
retro_sscr_1125,
Sus scrofa ENSSSCG000000297411 retrocopy
retro_sscr_634,
Sus scrofa ENSSSCG00000030014 2 retrocopies
retro_sscr_435, retro_sscr_909 ,
Tupaia belangeri ENSTBEG000000133804 retrocopies
retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,
Tarsius syrichta ENSTSYG000000001921 retrocopy
retro_tsyr_910,
Tursiops truncatus ENSTTRG000000157122 retrocopies
retro_ttru_1105, retro_ttru_134,
Vicugna pacos ENSVPAG000000009312 retrocopies
retro_vpac_283, retro_vpac_408,


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