RetrogeneDB ID:

retro_rnor_2340

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:6:2959858..2960748(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Eif4a2
Ensembl ID:ENSRNOG00000001815
Aliases:None
Description:Eukaryotic initiation factor 4A-II [Source:UniProtKB/Swiss-Prot;Acc:Q5RKI1]


Retrocopy-Parental alignment summary:






>retro_rnor_2340
ATCCCTTGTATTAAAGAGTCTGATGTGATTGCTCAAGCTCAGTCAGGTACTGACGAGACAGCCACATTTGCTATTTCCAC
CCTGCAGCAGTTGGAGACTGAGTTCAAGGAGACCCAAGCACTACTACTGGCCCCCACCAGAGGACTGGCTCAACAGATCC
AAAAGGTCATTTTGGCTCTTGGAGATTATATGGGAGCACCTTGTCATGCTTGCATTGGAGGGACCAATGTTTGAGATGAA
GTGCTGACGTTGCAGGCTGAAGCCCCTCATTGTTGTTGGTACTCCCGGGAGAGTGTTTGGTATGCTAAACAGAAGATCCC
CTTCTCCAAAATGGATCAAAATGTTTGTTTTGGATGAAGCACATGAAATGTTGAACCGAGGGTTTAAGGATCAGATCTAT
GAGATTTTCCAAAAATTAAATACAAGTATTCAGGTTCTGTTGCCTTCTGCCACACGCCAACTGATGTGCTAGAAGTGACC
AAGACATTCATGAGAGATCCGACTCGAATTCTGGTGAGGAAGGAAGAGTTGACCCTTGAAGGAATTGAACAATTTTATAT
TAATGTTGAGCGAGAAAAGTGGAAGCTGGGCACTCTTTGTGATGTGTATGAGACTTTGACTATCACACAAGCAGTCATTT
TTCTCAATACAAGGTGCAAGGTGGACTGGCTCACAGAGAAAAAGCATGCCAGGGACTTCAGAGTCTCTGCTCTACATGGT
GACATGGACCAGAAGGAACGAGATGTCATCTACGAGAGTTCCTGTCAGAGTCAAGCCCTGTTCTGATCACTACTGACTTG
TTGGCTCATGGGATTGACATGCAACAAGTGTCCTTGGTTATAAACTATGATCTACCTACCAATCGTGAAAACTATATTCA
CAGGAGTGGC

ORF - retro_rnor_2340 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.11 %
Parental protein coverage: 73.22 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHA
IPCIK..DVIAQAQSGT..TATFAIS.LQQLE.EFKETQAL.LAPTR.LAQQIQKVILALGDYMGA.CHA
RetrocopyIPCIKESDVIAQAQSGTDETATFAISTLQQLETEFKETQALLLAPTRGLAQQIQKVILALGDYMGAPCHA
ParentalCIGGTNVRNEMQKLQAEAPH-IVVGTPG-RVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQ
CIGGTNV..E...LQAEAPH......PG.RVF.MLNRR..SPKWIKMFVLDEA.EML.RGFKDQIYEIFQ
RetrocopyCIGGTNV*DEVLTLQAEAPH<LLLVLPG<RVFGMLNRRSPSPKWIKMFVLDEAHEMLNRGFKDQIYEIFQ
ParentalKLNTSIQVVLLSAT-MPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETL
KLNTSIQV.L.SAT..PTDVLEVTK.FMRDP.RILV.KEELTLEGI.QFYINVERE.WKL.TLCD.YETL
RetrocopyKLNTSIQVLLPSAT<TPTDVLEVTKTFMRDPTRILVRKEELTLEGIEQFYINVEREKWKLGTLCDVYETL
ParentalTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVI-MREFRSGSSRVLITTDLLARGIDVQ
TITQAVIFLNTR.KVDWLTEK.HARDF.VSALHGDMDQKERDVI..REF.S.SS.VLITTDLLA.GID.Q
RetrocopyTITQAVIFLNTRCKVDWLTEKKHARDFRVSALHGDMDQKERDVI<LREFLSESSPVLITTDLLAHGIDMQ
ParentalQVSLVINYDLPTNRENYIHRIG
QVSLVINYDLPTNRENYIHR.G
RetrocopyQVSLVINYDLPTNRENYIHRSG

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 1 .08 RPM 364 .01 RPM
SRP017611_kidney 1 .12 RPM 270 .82 RPM
SRP017611_liver 0 .40 RPM 89 .09 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2340 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2340 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2340 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147242 retrocopies
Canis familiaris ENSCAFG000000136591 retrocopy
Cavia porcellus ENSCPOG000000111831 retrocopy
Dasypus novemcinctus ENSDNOG000000115025 retrocopies
Echinops telfairi ENSETEG000000185653 retrocopies
Homo sapiens ENSG000001569762 retrocopies
Gorilla gorilla ENSGGOG000000058672 retrocopies
Macropus eugenii ENSMEUG000000117371 retrocopy
Microcebus murinus ENSMICG000000073771 retrocopy
Macaca mulatta ENSMMUG000000037022 retrocopies
Nomascus leucogenys ENSNLEG000000066331 retrocopy
Oryctolagus cuniculus ENSOCUG000000050113 retrocopies
Otolemur garnettii ENSOGAG000000107292 retrocopies
Ochotona princeps ENSOPRG000000041701 retrocopy
Pongo abelii ENSPPYG000000143842 retrocopies
Pan troglodytes ENSPTRG000000157181 retrocopy
Rattus norvegicus ENSRNOG00000001815 2 retrocopies
retro_rnor_1163, retro_rnor_2340 ,
Rattus norvegicus ENSRNOG000000306283 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
Tupaia belangeri ENSTBEG0000000226811 retrocopies
Takifugu rubripes ENSTRUG000000056602 retrocopies
Tarsius syrichta ENSTSYG000000130503 retrocopies



Copyright © RetrogeneDB 2014-2017