RetrogeneDB ID: retro_itri_581

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393303.1:3876663..3877041(+)
• Located in intron of: ENSSTOG00000014687

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSSTOG00000001675
• Aliases: None
• Description: cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]

Sequence

>retro_itri_581
GTTCTCTTCTGTTAAAGTGATTTAAAAAAAAGACAAATAACTGTAGAGGAGGCAAAGCAGATCTTGGTGGCAGGTGATAC
TGTAGAGGACTCTTACACATCTTTTGTGAAGTTGCTGCATGTGAATAATTGCCAGTATGCTTTGTACACTGCCACACATG
AAACAAAACAGTTCAATAAAAAAGTCTTTTATTTATATTCTAGGATCTTGAAACTGTACCCTTAAAAAGATGATTTATAC
TAGCTCTAAAGATGCCATTAAAAAGAATTTACAGGTATTAAACTCAAGTGGCAAGTAAATGGCTTGGATGATATTAAGAA
CCATTCAACATCTGGAAAGAAATTGGGAGGCCACACAGTAATTTCACTTAAATAAAAA

Alignment

ORF - retro_itri_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 77.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLFCLSDDKR-QIIVEEAKQILVGDIGDTVEDPYTSFVKLLPLNDCRYALYDATYETKESKKE-DLVFIF
          VLFC.SD....QI.VEEAKQILV...GDTVED.YTSFVKLL..N.C.YALY.AT.ETK...K...L.FIF
Retrocopy VLFC*SDXXXXQITVEEAKQILVA--GDTVEDSYTSFVKLLHVNNCQYALYTATHETKQFNKK<SLLFIF

Parental  WAPESAP-LKSKMIYASSKDAIKK-KFTGIKHEWQVNGLDDIKDRSTLGEKLGGNVVVSLEGK
          ...E..P.LK.KMIY.SSKDAIKK..FTGIK..WQVNGLDDIK..ST.G.KLGG..V.SL..K
Retrocopy *DLETVP<LK-KMIYTSSKDAIKK<EFTGIKLKWQVNGLDDIKNHSTSGKKLGGHTVISLK*K

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_581 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_581 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 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015508	1 retrocopy	retro_amel_1347,
Canis familiaris	ENSCAFG00000032562	1 retrocopy	retro_cfam_1006,
Cavia porcellus	ENSCPOG00000008996	1 retrocopy	retro_cpor_1003,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Felis catus	ENSFCAG00000008480	2 retrocopies	retro_fcat_1223, retro_fcat_1395,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
Loxodonta africana	ENSLAFG00000010579	1 retrocopy	retro_lafr_1041,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Microcebus murinus	ENSMICG00000009237	1 retrocopy	retro_mmur_493,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Otolemur garnettii	ENSOGAG00000032321	1 retrocopy	retro_ogar_2346,
Pteropus vampyrus	ENSPVAG00000002798	1 retrocopy	retro_pvam_398,
Rattus norvegicus	ENSRNOG00000045892	1 retrocopy	retro_rnor_684,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Sus scrofa	ENSSSCG00000001959	2 retrocopies	retro_sscr_1198, retro_sscr_327,
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,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,