RetrogeneDB ID: retro_cfam_1006

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:12639188..12639481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSCAFG00000032562
• Aliases: None
• Description: cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]

Sequence

>retro_cfam_1006
AAAGAAATAATCGTAACAAAAGCGAAACAAATCTTGGTGGGTGACACTAATGATACTGTAGAGGACCCCTACTCATCTTT
TGTGAAGTTGCTATCTCTGAATGATTGCCAATTTGCTTTGTATGATACCACACTCACAACAAGAGTCTGAGAAAGAAGAT
CTAGAATTTAAGTTCTGGGGTCCTGAACGTGTGTCTTTACAAAGCAAGATGATCTATTAGCACTGAAGATGTCATTAAAA
AGAAATTTACAGGCATTAAACATAAGTGGCAAGTAAATGGTATGGATGATATT

Alignment

ORF - retro_cfam_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.75 %
• Parental protein coverage: 59.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQIIVEEAKQILVGDIGDTVEDPYTSFVKLLPLNDCRYALYDATYETK-ESKKEDLVFIFWAPESAPLKS
          ..IIV..AKQILVGD..DTVEDPY.SFVKLL.LNDC..ALYD.T..T....K...L.F.FW.PE...L.S
Retrocopy KEIIVTKAKQILVGDTNDTVEDPYSSFVKLLSLNDCQFALYDTTLTTR>SEKED-LEFKFWGPERVSLQS

Parental  KMIY-ASSKDAIKK-KFTGIKHEWQVNGLDDI
          KMIY....K...K..KFTGIKH.WQVNG.DDI
Retrocopy KMIY<LALKMSLKR<KFTGIKHKWQVNGMDDI

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
SRP012049_cerebellum	0.04 RPM	84.84 RPM
SRP017611_brain	0.08 RPM	70.58 RPM
SRP017611_kidney	0.20 RPM	65.18 RPM
SRP017611_liver	0.22 RPM	24.65 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1006 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1006 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015508	1 retrocopy	retro_amel_1347,
Canis familiaris	ENSCAFG00000024955	6 retrocopies	retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
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,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,