RetrogeneDB ID: retro_btau_1382

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:60732027..60732400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL1
• Ensembl ID: ENSBTAG00000021455
• Aliases: None
• Description: Cofilin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9F7]

Sequence

>retro_btau_1382
GAGGTGAAGAACCACAAGAAAGTGGTGCTTTTATTTCTGAGTAAGGACAGGAAGATCCTCTGGGAGGAGGGCCAGGAGAT
CCTGGTAGGTAATGTAGACCAGGCTGATGATGACTACTTGCCCACTTAGGCAGGGCACCACCGGAGGAGGGCTGCCACTA
CATCCTCTATGATGCAAACTAGAAGACCAAGGGGAGTGAAAAGAGGATCTGGTACTTATCTTCTGGACCCCTGAGTCTGC
ATTTGTTAAGAGCAGAATGATCTATGCCAGCTCCAAGGACCCCATCAAGAAGAAGCTGAAGGGGATCAAGCATGAATTAT
GAGCAAACTGGTATGAGGAAGTCAAGGACTACTCTACCCTAGCAGAGAAACTG

Alignment

ORF - retro_btau_1382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYAT-FVKMLPDKDCRYALYDATYETKESKK
          EVK..KK.VL..LS.D.K.I..EEG.EILVG.V.Q..DD...T......P...C.Y.LYDA...TK.S.K
Retrocopy EVKNHKKVVLLFLSKDRK-ILWEEGQEILVGNVDQADDDYLPT<LGRAPPEEGCHYILYDAN*KTKGSEK

Parental  -EDLVFIFWAPECAPLKSKMIYASSKDAIKKKLTGIKHELQANCYEEVKDRCTLAEKL
          .EDLV.IFW.PE.A..KS.MIYASSKD.IKKKL.GIKHEL.AN.YEEVKD..TLAEKL
Retrocopy <EDLVLIFWTPESAFVKSRMIYASSKDPIKKKLKGIKHEL*ANWYEEVKDYSTLAEKL

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
ERP005899_liver	0.00 RPM	62.58 RPM
ERP005899_muscle	0.00 RPM	525.67 RPM
SRP017611_brain	0.00 RPM	401.89 RPM
SRP017611_kidney	0.00 RPM	229.03 RPM
SRP017611_liver	0.00 RPM	132.67 RPM
SRP030211_testis	0.00 RPM	128.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1382 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1382 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_660

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
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,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
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,
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,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Ictidomys tridecemlineatus	ENSSTOG00000027968	4 retrocopies	retro_itri_144, retro_itri_1456, retro_itri_1734, retro_itri_685,