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






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
SRP017611_brain 1 .08 RPM 364 .01 RPM
SRP017611_kidney 1 .12 RPM 270 .82 RPM
SRP017611_liver 0 .40 RPM 89 .09 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_2340 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

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
retro_btau_258, retro_btau_522,
Canis familiaris ENSCAFG000000136591 retrocopy
retro_cfam_378,
Cavia porcellus ENSCPOG000000111831 retrocopy
retro_cpor_639,
Dasypus novemcinctus ENSDNOG000000115025 retrocopies
retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi ENSETEG000000185653 retrocopies
retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens ENSG000001569762 retrocopies
retro_hsap_593, retro_hsap_878,
Gorilla gorilla ENSGGOG000000058672 retrocopies
retro_ggor_525, retro_ggor_712,
Macropus eugenii ENSMEUG000000117371 retrocopy
retro_meug_237,
Microcebus murinus ENSMICG000000073771 retrocopy
retro_mmur_525,
Macaca mulatta ENSMMUG000000037022 retrocopies
retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys ENSNLEG000000066331 retrocopy
retro_nleu_2589,
Oryctolagus cuniculus ENSOCUG000000050113 retrocopies
retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii ENSOGAG000000107292 retrocopies
retro_ogar_2830, retro_ogar_943,
Ochotona princeps ENSOPRG000000041701 retrocopy
retro_opri_498,
Pongo abelii ENSPPYG000000143842 retrocopies
retro_pabe_596, retro_pabe_677,
Pan troglodytes ENSPTRG000000157181 retrocopy
retro_ptro_437,
Rattus norvegicus ENSRNOG00000001815 2 retrocopies
retro_rnor_1163, retro_rnor_2340 ,
Rattus norvegicus ENSRNOG000000306283 retrocopies
retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
retro_itri_858,
Tupaia belangeri ENSTBEG0000000226811 retrocopies
retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes ENSTRUG000000056602 retrocopies
retro_trub_14, retro_trub_6,
Tarsius syrichta ENSTSYG000000130503 retrocopies
retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,


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