RetrogeneDB ID:

retro_rnor_1888

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:3:58096030..58096415(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Skp1
Ensembl ID:ENSRNOG00000005828
Aliases:Skp1, Skp1a
Description:S-phase kinase-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6PEC4]


Retrocopy-Parental alignment summary:






>retro_rnor_1888
CAACAATGTGAGGGAGAGATAGAAACTTGATTAGAAATTGCCAAGTAATATGTAAGGCCATGTTTGGAAGATTCAAGAGC
AGTGGCAGAAGGAAATGATGTATGTTTACCTAATGTTGATACAGCAGCACTAAAGAAGGTCATTCAGTAATGTGCCCACC
ACAGAGATGACCTTCCTTGTCCCAGGGAAGATGAGAACAAAGAGAAGAAGACAGACGATATCCCCGTTTGGGACTAAGAG
TCCTGAAAGTCAACCAAGGAATGCTTTGTGAAGTTATTCTGGCTGCAAAATACTCGACATCAAAGATTTGCTCGATGTCT
TATGCAAGGCTGTTTCCAGTAAGACCAAGGAGAAGGAACGCCCTGAGAAGACTTACACATCCTTT

ORF - retro_rnor_1888 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.35 %
Parental protein coverage: 81.6 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDE
Q...GEI.E...EIAK..V.....LED.....EG.D..V.LPNV..A.LKKVIQ.C.HH.DD.P.P..DE
RetrocopyQQCEGEI-ET*LEIAK*YV--RPCLEDSRAVAEGND--VCLPNVDTAALKKVIQ*CAHHRDDLPCPREDE
ParentalNKEKRTDDIPVWDQE-FLKVDQGTLFELILAANY-LDIKGLLDVTCKTVANMIKGK-TPEEIRKTF
NKEK.TDDIPVWD.E..LKV.QG.L.E.ILAA.Y.LDIK.LLDV.CK.V....K.K..PE.....F
RetrocopyNKEKKTDDIPVWD*E<VLKVNQGMLCEVILAAKY<LDIKDLLDVLCKAVSSKTKEKERPEKTYTSF

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
SRP017611_brain 0 .00 RPM 277 .95 RPM
SRP017611_kidney 0 .00 RPM 493 .22 RPM
SRP017611_liver 0 .00 RPM 143 .96 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1888 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1888 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1888 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 75 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000251915 retrocopies
Canis familiaris ENSCAFG000000009945 retrocopies
Callithrix jacchus ENSCJAG000000136131 retrocopy
Echinops telfairi ENSETEG000000075605 retrocopies
Homo sapiens ENSG0000011355810 retrocopies
Gorilla gorilla ENSGGOG000000229307 retrocopies
Loxodonta africana ENSLAFG000000168321 retrocopy
Microcebus murinus ENSMICG000000175883 retrocopies
Myotis lucifugus ENSMLUG0000002291913 retrocopies
Monodelphis domestica ENSMODG000000141684 retrocopies
Otolemur garnettii ENSOGAG000000287078 retrocopies
Pongo abelii ENSPPYG000000157837 retrocopies
Rattus norvegicus ENSRNOG00000005828 6 retrocopies



Copyright © RetrogeneDB 2014-2017