RetrogeneDB ID:

retro_sscr_460

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:15:70605460..70606005(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSSSCG00000029642
Aliases:None
Description:ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]


Retrocopy-Parental alignment summary:






>retro_sscr_460
ATGGTTTGCTATTCACTTGGCCCAGAAAACCCAACAAAATCATGCAAATCAAGAGGTTCAAATCTTTGCCTTCACTTCAG
AAACATTCATGAAACTGTCCAGGCCATTAAGGGTATACATATTCAAAAAGCCACAAAGTAGCCGAAGGATGTCACTCTAC
AGAAGTAATATGTGCCATTCCATCATTATGGTGGTGAAGTTGGTAGCTGTGCCCAGGCCAAAAAGCAGGGCTGGGCACAG
GGTCGGTGACCCAAAAAGAGTGCTGAATTTTTCTTGCACATGCTCAAAAAATGCAGAGTAATGTTGAACGTAAGGACTTA
GATGTAGATTCTCTAGTCATTGAGCACATCCAGGTGAACAAAGCCCCCAATATGTGGCGCAGGACTTACAGAGCTCATGG
TCTGAGCCCTTATATGAGTTCTCCCTGCCACATTGAGATGATCCTTACTGAAAAAGAGCAGATTGTTCCTAAGCCAGGAA
AGGATGTTGCACAGAAGAAAAAGATATCCCAGAAGAAAGTGAAGAAACAAAAACTTATGGTCCAG

ORF - retro_sscr_460 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.63 %
Parental protein coverage: 99.45 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDFTLQKQCVPFRRYNG-VGRC
MV.YSL.PENPTKSCKSRGSNL..HF.N..ET.QAIKG.HI.KATK..KD.TLQK..VPF..Y.G.VG.C
RetrocopyMVCYSLGPENPTKSCKSRGSNLCLHFRNIHETVQAIKGIHIQKATK*PKDVTLQK*YVPFHHYGGEVGSC
ParentalAQAKQWGWTQGRWPKKSAEFLLHMLKNA-ESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPY
AQAK..GW.QGR.PKKSAEF.LHMLK....SN.E.K.LDVDSLVIEHIQVNKAP.M.RRTYRAHG...PY
RetrocopyAQAKKQGWAQGR*PKKSAEFFLHMLKKC<QSNVERKDLDVDSLVIEHIQVNKAPNMWRRTYRAHG-LSPY
ParentalMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMAR
MSSPCHIEMILTEKEQIVPKP...VAQKKKISQKK.KKQKLM..
RetrocopyMSSPCHIEMILTEKEQIVPKPGKDVAQKKKISQKKVKKQKLMVQ

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 409 .48 RPM
SRP014902_testis 0 .14 RPM 1086 .45 RPM
SRP018288_heart 0 .00 RPM 699 .89 RPM
SRP018288_kidney 0 .00 RPM 518 .83 RPM
SRP018288_liver 0 .00 RPM 468 .70 RPM
SRP018288_lung 0 .00 RPM 447 .73 RPM
SRP018856_adipose 0 .02 RPM 2235 .01 RPM
SRP035408_brain 0 .10 RPM 1765 .53 RPM
SRP035408_liver 0 .09 RPM 949 .78 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_460 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_460 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_460 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 256 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Loxodonta africana ENSLAFG0000000556916 retrocopies
Macropus eugenii ENSMEUG0000001670926 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Sus scrofa ENSSSCG00000029642 30 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



Copyright © RetrogeneDB 2014-2017