RetrogeneDB ID: retro_itri_1629

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393593.1:1069174..1069560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004798
• Aliases: None
• Description: None

Sequence

>retro_itri_1629
GGGCCCTCCTGAACCCAGGAGCGCACCCTGGTTACAGTGAAGCCAGATGGGCACAGTGGCTGCTCATCGGAGCTGTGATC
CAGCACCTTGAGAGGCGGGGCTTCAAGCTGGTTGTCACAAGACACTGCAGGCCCTGAGAGTCCTTGCTGAACGCTACCAG
GACCTATAGAGGAAGCCCTTTCACCCAGCCCTCATCAGCAACATGAGCTCTCGACCCAAGGTGGCCATGGTCTGGAAGGG
TACAATGTGGTCCGGACCTCAAGGGCCATGACAGGCACAGTGATTCCACCAAGGCTGCTCCTGGGACCCTCCGGGGAGAC
TGCAGCATTCTCGTCAGCAGAAACATCATTCACGCCAGTGACCCAGTGGAAGGGGCCCAGAGGGAT

Alignment

ORF - retro_itri_1629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.56 %
• Parental protein coverage: 83.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GPSWTQERTLVAVKPDG-VQRRLIGAVIQRFERRGFKLVGM-KMLQAPESILAEHYQDLQRKPFYPALIS
          GPS.TQERTLV.VKPDG..Q..LIGAVIQ..ERRGFKLV...K.LQA....LAE.YQDL.RKPF.PALIS
Retrocopy GPS*TQERTLVTVKPDG<AQWLLIGAVIQHLERRGFKLVVT<KTLQALR-VLAERYQDL*RKPFHPALIS

Parental  YMSSGPVVAMVW-EGYNVVRASRAMIG-HSDSTEAAPGTIRGDFSIHISRNIIHASDSVEGAQRE
          .MSS.P.VAMVW.EGYNVVR.SRAM.G.HSDST.AAPGT.RGD.SI..SRNIIHASD.VEGAQR.
Retrocopy NMSSRPKVAMVW<EGYNVVRTSRAMTG<HSDSTKAAPGTLRGDCSILVSRNIIHASDPVEGAQRD

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_1629 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1629 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 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000002690	1 retrocopy	retro_itri_675,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629 ,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,