RetrogeneDB ID:

retro_dnov_648

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_7192:302559..303239(-)
Located in intron of:ENSDNOG00000010843
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A2
Ensembl ID:ENSDNOG00000011502
Aliases:None
Description:eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284]


Retrocopy-Parental alignment summary:






>retro_dnov_648
GTACTGGACGAAGCTGATGAATGCTGAGCCGTGGATTCAAAGACCATATCTATGATATATTCCAAAAACTCAACAGCAAT
ACCTAGGTGGTTTTGTTGTCTGCTACAATGCCTTCCGATGTGCTCGAGGTGACTAAGAAGTTCATGAGGGACCCCATTCG
GATTCTCGTCAAGAAGGAAGAGTTGACGCTGGAGGGTATCCGCCAGTTCTACATCAGTGTGGAATGAGAGGAATGGAAGC
TGGACACATTGTGTGACTTGTATGAGACCCTGACCATCACCCAAGCAGTCATCTTCATCAACACCCGAAGAAAGATTGAT
TGGCTTACTGAGAAGATGCATGCCCGAGACTTCACTGTCTCTGCTATGCATGGCGACATGGATCAAAAGGAACGAGATGT
GATCATGAGGGAGTTCCGTTCTGGTTCTAGCAGAGTACTGATCACCACTGACCTGCTGGCCAGAGGCATTGATGTGCAGC
AGGTTTCTTTAGTCATCAACTATGACCTTCCCACCAACAGGGAAAACTATATCCACAGAATCGGTCGAGGTGGACGTTTT
GGCCGTAAGGGTGTGGCTATTAACATGGTGACAGAAGAAGACAAGAGGACTCTTCGAGACATTGAGACCTTCTACAACAC
CTCCATTGAGGAGATGCCCCTCAGTGTTGCTGACCTCATC

ORF - retro_dnov_648 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.23 %
Parental protein coverage: 55.77 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVLDEADE-MLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQ
VLDEADE.MLSRGFKD.IY.IFQKLN....VVLLSATMP.DVLEVTKKFMRDPIRILVKKEELTLEGI.Q
RetrocopyVLDEADE<MLSRGFKDHIYDIFQKLNSNT*VVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQ
ParentalFYINVEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREF
FYI.VE.EEWKLDTLCDLYETLTITQAVIF.NTRRK.DWLTEKMHARDFTVSA.HGDMDQKERDVIMREF
RetrocopyFYISVE*EEWKLDTLCDLYETLTITQAVIFINTRRKIDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF
ParentalRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIE
RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAIN.VTEEDKR.LRDIE
RetrocopyRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIE
ParentalTFYNTTVEEMPMNVADLI
TFYNT..EEMP..VADLI
RetrocopyTFYNTSIEEMPLSVADLI

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
SRP012922_ascending_colon 190 .00 RPM 303 .18 RPM
SRP012922_cerebellum 69 .01 RPM 516 .06 RPM
SRP012922_heart 48 .73 RPM 255 .93 RPM
SRP012922_kidney 95 .83 RPM 222 .60 RPM
SRP012922_liver 104 .65 RPM 91 .65 RPM
SRP012922_lung 104 .77 RPM 268 .34 RPM
SRP012922_quadricep_muscle 35 .48 RPM 341 .50 RPM
SRP012922_spleen 126 .94 RPM 238 .08 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_648 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 21 parental genes, and 49 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 ENSDNOG00000011502 5 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 ENSRNOG000000018152 retrocopies
retro_rnor_1163, retro_rnor_2340,
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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