RetrogeneDB ID: retro_btau_116

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:44229782..44230328(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000017191
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSBTAG00000034992
• Aliases: None
• Description: Malignant T-cell-amplified sequence 1 [Source:UniProtKB/Swiss-Prot;Acc:Q2KIE4]

Sequence

>retro_btau_116
ATGTTCAAGAAATTTGATGAAAAAGAAAACGTGTCGAACTGTATCCAGTTGAAAACTTCCGTTATTAAGGGCATTAAGAA
CCAGTTGATGGAGCAGTTTCCCGGCATCGAACCGTGGCTGAACCAAATCATGCCAAAGAAGGATCCGGTCAAAATAGTGC
GATGCCACGAGCACATAGAAATCCTCACGGTGAACGGGGAGCTGCTGTTCTTCAGGCAAAGGGAAGGGCCTTTCTACCCA
ACGCTGAGGTTGCTGCACAAGTATCCGTTCATCCTGCCCCGCCAGCAGGTGGACAAGGGAGCCATCAAGTTCGTGCTCAG
CGGAGCCAACATCATGTGCCCAGGCCTGACCTCGCCGGGGGCCCGCCTCTTCCCCGCCGCAGTGGACACGGTGGTGGCGA
TCATGGCGGAGGGAAAGCAGCACGCTCTGTGCGTGGGCGTCATGAAGATGTCCGCGGACGAGATCGAGAAAGTCAACAAA
GGAATCGGCATCGAGAACATCCATTACCTCAATGACGGGCTGTGGCACATGAAGACGTACAAGTGA

Alignment

ORF - retro_btau_116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
          MFKKFDEKENVSNCIQLKTSVIKGIKNQL.EQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
Retrocopy MFKKFDEKENVSNCIQLKTSVIKGIKNQLMEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQ
          FRQREGPFYPTLRLLHKYPFILP.QQVDKGAIKFVLSGANIMCPGLTSPGA.L.PAAVDT.VAIMAEGKQ
Retrocopy FRQREGPFYPTLRLLHKYPFILPRQQVDKGAIKFVLSGANIMCPGLTSPGARLFPAAVDTVVAIMAEGKQ

Parental  HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          HALCVGVMKMSA..IEKVNKGIGIENIHYLNDGLWHMKTYK
Retrocopy HALCVGVMKMSADEIEKVNKGIGIENIHYLNDGLWHMKTYK

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	9.52 RPM	23.58 RPM
ERP005899_muscle	33.79 RPM	13.88 RPM
SRP017611_brain	20.78 RPM	12.33 RPM
SRP017611_kidney	29.16 RPM	8.36 RPM
SRP017611_liver	18.88 RPM	11.93 RPM
SRP030211_testis	11.40 RPM	1.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_btau_116 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW425451	44229745	44230009	100	264	0	264
DY210510	44229774	44230027	100	253	0	253

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_116 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_94

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116 ,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Felis catus	ENSFCAG00000008448	2 retrocopies	retro_fcat_1009, retro_fcat_310,
Macropus eugenii	ENSMEUG00000014328	1 retrocopy	retro_meug_1518,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pongo abelii	ENSPPYG00000020687	2 retrocopies	retro_pabe_1786, retro_pabe_1833,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138,