RetrogeneDB ID: retro_btau_1048

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 24:43149794..43150376(+)
• Located in intron of: ENSBTAG00000002125

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSBTAG00000033331
• Aliases: CHMP1A, PCOLN3
• Description: charged multivesicular body protein 1a [Source:RefSeq peptide;Acc:NP_001178189]

Sequence

>retro_btau_1048
ATGGAGAAACACCTGTTCAACTTAAAGTTCGCGGCCAAAGAACTGGGCAGGAGTGCTAAAAAATGCGACAAGGAGGAAAA
GGCCGAAAAGGCCAAGATTAAAAAGGCCATTCAGAAGGGCAATATGGAAGTTGCGAGGATTCACGCCGAGAACGCGATTC
GCCAGAAGAACCAGGCAGTGAATTTCTTGAGGATGAGCGCGCGGGTGGACGCGGTGGCCGCCAGGGTCCAGACGGCCGTG
ACGATGGGCAAGGTGACCAAGTCGATGGCCGGAGTGGTTAAGTCGATGGACGCGACGTTGAAGACCATGAACCTCGAGAA
GATCTCCGCCCTGATGGACAAGTTCGAGCACCAGTTCGAGACGCTGGACGTTCAGACGCAGCAGATGGAGGACACGATGA
GCAGCACGACGACGCTGACCACTCCCCAGGGCCAGGTGGACATGCTGCTGCAGGAAATGGCAGACGAGGCCGGCCTCGAC
CTCAACATGGAGCTGCCGCAGGGCCAGACCGGCTCCGTGGGGACGAGCGTAGCCTCGGCCGAGCAGGACGAGCTGTCCCA
GAGGTTGGCCCGCCTGCGGGAC

Alignment

ORF - retro_btau_1048 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVD
          M...LF.LKF.AK.L...AKK..K..KAE.AK.KKA.Q..N.E.AR..AENAIR.KN..VN.LRM..RVD
Retrocopy MEKHLFNLKFAAKELGRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVD

Parental  AVASKVQTAVTMKGVTKNMAQVTKALDRALSTMDLQKVSAVMDRFEQQVQNLDVHTSVMEDSMSSATTLT
          AVA..VQTAVTM..VTK.MA.V.K..D..L.TM.L.K.SA.MD.FE.Q...LDV.T..MED.MSS.TTLT
Retrocopy AVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLT

Parental  TPQEQVDSLILQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          TPQ.QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
Retrocopy TPQGQVDMLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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	1.73 RPM	11.25 RPM
ERP005899_muscle	44.87 RPM	45.19 RPM
SRP017611_brain	14.53 RPM	38.92 RPM
SRP017611_kidney	19.03 RPM	35.92 RPM
SRP017611_liver	14.57 RPM	26.13 RPM
SRP030211_testis	9.05 RPM	57.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_btau_1048 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE589019	43149766	43150053	99	284	3	281
DY133038	43149769	43149953	97.8	176	3	171
DY148551	43149841	43150009	99.5	167	1	166

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1048 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048 ,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,