RetrogeneDB ID:

retro_itri_496

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393296.1:477908..478193(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFS6
Ensembl ID:ENSSTOG00000003715
Aliases:None
Description:NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7713]


Retrocopy-Parental alignment summary:






>retro_itri_496
CGCAACCTTCTGTGGGCTGCTGGTCCTGCCCCGGGCTGGGCAGGCAGGGTGCAATTGTCCCCGACAGGGGAGAAGGTCAC
ACACACCAGCCAGGTGTATGATGATAAAGACTACAGGAAATTTTGGTTTGTAGGTCACCAGAAAGGGGTGAATGAAAACT
TAGCCACTGATTCGATAGCAGAGCAGACTGTGAGTGAGGTGGACCACTGGGTGATCATGTGTGACAGCAGTGGGGTGGCC
CAGGGCAAGGTGTTCATAAACCTGGAAAAAGAACCAAAACCTGGC

ORF - retro_itri_496 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.98 %
Parental protein coverage: 81.9 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRQLLWLPRVARSFGVRV--SPTGEKVTHTGQVYDDKDYRKIRFVGRQKEVNENFAIDLIAEQPVSEVDHR
R.LLW....A.....RV..SPTGEKVTHT.QVYDDKDYRK..FVG.QK.VNEN.A.D.IAEQ.VSEVDH.
RetrocopyRNLLWAAGPAPGWAGRVQLSPTGEKVTHTSQVYDDKDYRKFWFVGHQKGVNENLATDSIAEQTVSEVDHW
ParentalVISCDGGGGALGHPKVYINLDKETKTG
VI.CD..G.A.G..KV.INL.KE.K.G
RetrocopyVIMCDSSGVAQG--KVFINLEKEPKPG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_496 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_496 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 19 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000109302 retrocopies
retro_amel_213, retro_amel_228,
Bos taurus ENSBTAG000000099142 retrocopies
retro_btau_302, retro_btau_333,
Callithrix jacchus ENSCJAG000000193821 retrocopy
retro_cjac_1552,
Equus caballus ENSECAG000000216903 retrocopies
retro_ecab_701, retro_ecab_838, retro_ecab_917,
Homo sapiens ENSG000001454941 retrocopy
retro_hsap_2838,
Latimeria chalumnae ENSLACG000000046251 retrocopy
retro_lcha_95,
Loxodonta africana ENSLAFG000000057081 retrocopy
retro_lafr_5,
Myotis lucifugus ENSMLUG000000168881 retrocopy
retro_mluc_1750,
Macaca mulatta ENSMMUG000000044471 retrocopy
retro_mmul_1473,
Monodelphis domestica ENSMODG000000014251 retrocopy
retro_mdom_207,
Mus musculus ENSMUSG000000216061 retrocopy
retro_mmus_3044,
Nomascus leucogenys ENSNLEG000000111991 retrocopy
retro_nleu_1593,
Oryctolagus cuniculus ENSOCUG000000045812 retrocopies
retro_ocun_1011, retro_ocun_1624,
Pongo abelii ENSPPYG000000153231 retrocopy
retro_pabe_2350,
Pan troglodytes ENSPTRG000000167061 retrocopy
retro_ptro_1924,
Rattus norvegicus ENSRNOG000000233871 retrocopy
retro_rnor_1619,
Rattus norvegicus ENSRNOG000000493941 retrocopy
retro_rnor_1618,
Sarcophilus harrisii ENSSHAG000000177791 retrocopy
retro_shar_176,
Ictidomys tridecemlineatus ENSSTOG00000003715 1 retrocopy
retro_itri_496 ,


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