RetrogeneDB ID: retro_itri_1231

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393408.1:3631365..3631684(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSSTOG00000007989
• Aliases: None
• Description: mitochondrial ribosomal protein S18C [Source:HGNC Symbol;Acc:16633]

Sequence

>retro_itri_1231
CCCAGAACTCACAGGGTGCTATGGAGAAGAAGTTGTTCACTATACAAACTGGTAACCAGCATCAGTAACCCACATGTTCC
AATGGAAAAATCTCTTAATAAATGTATCTGTGTGAGAAGTGTGTAGATTATAAAAATATACAGTTTTTCTCCCAGTTTAT
TTCTCCATTTACTGAACATATTTATGGAAATCATATAACAAGCCTTTATAAGAAGAAACAAGAAAATTATAAAAGTGAGA
CCTCAATAATAGGATTTATACCATTATACATAAGGATCTTGCATATCTCAAAGACTTTAAAGTTTGTAACATCGAATAT

Alignment

ORF - retro_itri_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.9 %
• Parental protein coverage: 79.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGTRAVLWRRGCSQYKQGTSNEDLPVPMENPYKEPLKKCI-LCEKRVDYKNVQLLSQFISPFTGCIYGRH
          P.T..VLWRR.CS.YK..TS.....VPME......L.KCI.LCEK.VDYKN.Q..SQFISPFT..IYG.H
Retrocopy PRTHRVLWRRSCSLYKLVTSISNPHVPME----KSLNKCI<LCEKCVDYKNIQFFSQFISPFTEHIYGNH

Parental  ITGLCGKKQKEITKAIKRAQIMGFMP-VTYKDPAYLKDPKVCNIKY
          IT.L..KKQ...........I.GF.P....KD.AYLKD.KVCNI.Y
Retrocopy ITSLYKKKQENYK---SETSIIGFIP<IIHKDLAYLKDFKVCNIEY

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1231 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1231 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Macaca mulatta	ENSMMUG00000015353	4 retrocopies	retro_mmul_2203, retro_mmul_2494, retro_mmul_655, retro_mmul_793,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231 ,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,