RetrogeneDB ID:

retro_sscr_886

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:6:119708811..119709253(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSSSCG00000025192
Aliases:None
Description:ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]


Retrocopy-Parental alignment summary:






>retro_sscr_886
ATCAATGCAGAACTCTATTTCATTGGAAAGAAGATGCTCCGGGCTGACAAAATGGTAGGGAAATAGAAAGGGACTGGCTT
ACCCTTTCTGTAGTCATGTACAGCACGCCATCAAGAGTGTCACCCTGGCTTCCACCGCAAGATGAGATTCTGTGCATGCT
CACTCCCCTGTCAATGATGTTATTCAGGAGAATGGGTCCCTTGCTGAAATCCAAAATTTCTTGGGTGAAAAATATCTCAA
AAGTGTTTGGATGAAGCCAGGAGTTACTTGTTCAGTATCCCAAGTGCAGAAAAATGACTTAATTCTTGAGGGAAATGATG
GTGAAATTATATCAAATTCAGCTGTTTTGATTCAGCAAGCCACAACATTTAAAAACAAGGTTATCAGAAAATTTCTAGGT
GATATCTATGTCTCTGAAGAAACAATTCATCAAGCTGCTGAA

ORF - retro_sscr_886 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.1 %
Parental protein coverage: 79.17 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalINVELSLLGKKKKRLRVDK-WWGNRKELATVRTICSHVQNMIKGVTL-GFRYKMR-SVYAHFPINVVIQE
IN.EL...GKK...LR.DK.W.GNRK.LA.....CSHVQ..IK.VTL.GF..KMR.SV.AH.P.N.VIQE
RetrocopyINAELYFIGKKM--LRADK>W*GNRKGLAY--PFCSHVQHAIKSVTL<GFHRKMR>SVHAHSPVNDVIQE
ParentalNGSLVEIRNFLGEKYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLD
NGSL.EI.NFLGEKY...V.M.PGV.CSVSQ.QK..LILEGND.E..SNSA.LIQQATT.KNK.IRKFL.
RetrocopyNGSLAEIQNFLGEKYLKSVWMKPGVTCSVSQVQKNDLILEGNDGEIISNSAVLIQQATTFKNKVIRKFLG
ParentalGIYVSEKGTVQQADE
.IYVSE..T..QA.E
RetrocopyDIYVSEE-TIHQAAE

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 118 .79 RPM
SRP014902_testis 0 .00 RPM 511 .75 RPM
SRP018288_heart 0 .00 RPM 528 .95 RPM
SRP018288_kidney 0 .00 RPM 438 .94 RPM
SRP018288_liver 0 .00 RPM 412 .89 RPM
SRP018288_lung 0 .00 RPM 469 .83 RPM
SRP018856_adipose 0 .00 RPM 755 .73 RPM
SRP035408_brain 0 .00 RPM 390 .69 RPM
SRP035408_liver 0 .00 RPM 327 .05 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_886 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_886 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_886 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_867

Parental genes homology:
Parental genes homology involve 26 parental genes, and 471 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000318731 retrocopies
Bos taurus ENSBTAG000000145183 retrocopies
Canis familiaris ENSCAFG0000001600828 retrocopies
Callithrix jacchus ENSCJAG0000000072329 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Equus caballus ENSECAG000000164897 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Felis catus ENSFCAG0000001228434 retrocopies
Homo sapiens ENSG0000016368228 retrocopies
Gorilla gorilla ENSGGOG0000002279926 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Loxodonta africana ENSLAFG0000001202138 retrocopies
Macropus eugenii ENSMEUG000000167228 retrocopies
Microcebus murinus ENSMICG0000001677818 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Macaca mulatta ENSMMUG0000000855322 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Nomascus leucogenys ENSNLEG0000001710026 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Pongo abelii ENSPPYG0000001467510 retrocopies
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
Sus scrofa ENSSSCG00000025192 15 retrocopies
Tupaia belangeri ENSTBEG0000000604218 retrocopies
Vicugna pacos ENSVPAG000000020231 retrocopy



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