RetrogeneDB ID: retro_fcat_1395

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:48303021..48303499(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSFCAG00000008480
• Aliases: None
• Description: cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]

Sequence

>retro_fcat_1395
TCTGGAGTTACAAATGAACAACGATGTCAACAAAGTTGTTAATGATATGAAAGTAAGGAAATCTACACGAGATCAGAAAA
AAGAAAGAAACTCGTTCTCTTCCGTTTATGCGATGGCAAAAGAAATCACTGTTAGAGAAAGCAAAGCAGATGTTGGTGGG
TGACACTAGTGATATTGTAGAGGACCCCTACACATCTTTTGTGAAGTTGCTGTCTCTGAATGATTGCCAATTTGCTTGTA
TAATGCACATTCAAAACAAGAGTCTAAGAAAGAAGACCTAGTATTTAAATTCTGGGGTCCTGAAAGTGCACTTTATAACA
CGAGATGATATATGCTATCTCTAAAGATGCCATTAAAAAGAAATTTACAGATATTAAACTTAAGTTGCAAGTAAACGGCT
TGGATAATATTAAGGAGTATTCCTCACTTGGAGAGAAACAAAGGCAACATAGTGGTCCCACTTGAAGGAAACCCCTTA

Alignment

ORF - retro_fcat_1395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.29 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SGVT-VNDEVIKVFNDMKVRKSS-TQEEIKKRKKAVLFCLSDDKR-QIIVEEAKQILVGDIGDTVEDPYT
          SGVT..N..V.KV.NDMKVRKS..T..E..KRKK.VLF.L.D.KR.....E.AKQ.LVGD..D.VEDPYT
Retrocopy SGVT>MNNDVNKVVNDMKVRKST<TRSE--KRKKLVLFRLCDGKR<KSLLEKAKQMLVGDTSDIVEDPYT

Parental  SFVKLLPLNDCRYA-LYDATYETKESKKEDLVFIFWAPESA-PLKSKMIYASSKDAIKKKFTGIKHEWQV
          SFVKLL.LNDC..A.LY.A.....ESKKEDLVF.FW.PESA..L...MIYA.SKDAIKKKFT.IK...QV
Retrocopy SFVKLLSLNDCQFA<LYNA-HSKQESKKEDLVFKFWGPESA<TL*HEMIYAISKDAIKKKFTDIKLKLQV

Parental  NGLDDIKDRSTLGEK-LGGNVVVSLEGKPL
          NGLD.IK..S.LGEK..G..VV..LEG.PL
Retrocopy NGLDNIKEYSSLGEK>KGNIVV-PLEGNPL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	12.62 RPM
SRP017611_kidney	0.00 RPM	7.21 RPM
SRP017611_liver	0.00 RPM	8.19 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1395 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1395 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus 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 39 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 ,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
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,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,