RetrogeneDB ID: retro_itri_1456

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393493.1:2418125..2418611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL1
• Ensembl ID: ENSSTOG00000027968
• Aliases: None
• Description: cofilin 1 (non-muscle) [Source:HGNC Symbol;Acc:1874]

Sequence

>retro_itri_1456
AATGAAAGGACATTAAACTACTTAAGGGAGGAGGGCAAGGAGATCCTGGAAGACGTTGGCCAGACTGTGGATGACCCCTA
TGCCACATTTGTCAAGATGCAGCTAGACAAGGGCTGCTGCTGTGCCCTCTATAACACAACCTGCAAGAACTAGGAGGAGG
ACCTCGTGTTTATCTTCTGGGTCCCTGAGTCTGCACCTCTTAGGAACAAAATGGTCTATGCCAGTTCTAAGGATACCATC
GATAAGAAGCTGACAAAGGTCAAACATGAATTACAAGCAAACTGCCACAAGGAGGTCAACAACCACCATACCCTGGCAGA
GATGCTGCCAGATCAGCGCTGTCATCTCCCTGGAGGACAAGCCTTTGTGAGCCCCCTTCAGCCTCCTGCCTGGAGCATCT
GGCAGCCCCAGGCCTCCCTGGTGTGTGGGGGGGTTCAGGATGACCCCTTTCTGCCAGACTGGAGTAGCTAGGGGATCCCA
GCAGGG

Alignment

ORF - retro_itri_1456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.31 %
• Parental protein coverage: 72.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEDKKNIILEEGKEILVGDVGQTVDDPYATFVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAP
          .E...N...EEGKEIL..DVGQTVDDPYATFVKM..DK.C..ALY..T....E...EDLVFIFW.PESAP
Retrocopy NERTLNYLREEGKEILE-DVGQTVDDPYATFVKMQLDKGCCCALYNTTCKN*E---EDLVFIFWVPESAP

Parental  LKSKMIYASSKDAIKKKLTGIKHELQANCYEEVKDRCTLAEKLGG-SAVISLEGKPL-PPP-APCLEHLS
          L..KM.YASSKD.I.KKLT..KHELQANC..EV....TLAE.L...SAVISLE.KPL..PP.A.CLEHL.
Retrocopy LRNKMVYASSKDTIDKKLTKVKHELQANCHKEVNNHHTLAEMLPD>SAVISLEDKPL>EPPSASCLEHLA

Parental  -PRPAL--GGCRLPPSCQTGGAGGIPAG
          .P...L..GG....P........GIPAG
Retrocopy >PQASLVCGGVQDDPFLPDWSS*GIPAG

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_1456 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1456 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 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017334	2 retrocopies	retro_amel_583, retro_amel_816,
Bos taurus	ENSBTAG00000021455	1 retrocopy	retro_btau_1382,
Canis familiaris	ENSCAFG00000024955	6 retrocopies	retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
Callithrix jacchus	ENSCJAG00000001916	1 retrocopy	retro_cjac_347,
Equus caballus	ENSECAG00000019900	1 retrocopy	retro_ecab_442,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
Homo sapiens	ENSG00000172757	6 retrocopies	retro_hsap_2617, retro_hsap_287, retro_hsap_3333, retro_hsap_336, retro_hsap_384, retro_hsap_400,
Gorilla gorilla	ENSGGOG00000023183	5 retrocopies	retro_ggor_1832, retro_ggor_326, retro_ggor_357, retro_ggor_389, retro_ggor_397,
Microcebus murinus	ENSMICG00000012763	1 retrocopy	retro_mmur_703,
Myotis lucifugus	ENSMLUG00000024685	6 retrocopies	retro_mluc_1905, retro_mluc_2114, retro_mluc_216, retro_mluc_2218, retro_mluc_455, retro_mluc_507,
Macaca mulatta	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mustela putorius furo	ENSMPUG00000011502	2 retrocopies	retro_mputfur_1485, retro_mputfur_575,
Nomascus leucogenys	ENSNLEG00000005852	5 retrocopies	retro_nleu_139, retro_nleu_1494, retro_nleu_1571, retro_nleu_1777, retro_nleu_636,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Otolemur garnettii	ENSOGAG00000016503	8 retrocopies	retro_ogar_1442, retro_ogar_1581, retro_ogar_1648, retro_ogar_2192, retro_ogar_302, retro_ogar_405, retro_ogar_453, retro_ogar_828,
Pongo abelii	ENSPPYG00000003047	5 retrocopies	retro_pabe_1732, retro_pabe_2747, retro_pabe_316, retro_pabe_325, retro_pabe_386,
Pan troglodytes	ENSPTRG00000003895	5 retrocopies	retro_ptro_1764, retro_ptro_2146, retro_ptro_236, retro_ptro_298, retro_ptro_306,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Ictidomys tridecemlineatus	ENSSTOG00000001675	3 retrocopies	retro_itri_1313, retro_itri_581, retro_itri_632,
Ictidomys tridecemlineatus	ENSSTOG00000027968	4 retrocopies	retro_itri_144, retro_itri_1456 , retro_itri_1734, retro_itri_685,
Tursiops truncatus	ENSTTRG00000016931	2 retrocopies	retro_ttru_1256, retro_ttru_598,