RetrogeneDB ID: retro_btau_1566

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:31755370..31755682(-)
• Located in intron of: ENSBTAG00000013184

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMGT1
• Ensembl ID: ENSBTAG00000025297
• Aliases: MMGT1, TMEM32
• Description: membrane magnesium transporter 1 precursor [Source:RefSeq peptide;Acc:NP_001073098]

Sequence

>retro_btau_1566
CGTTCTTATATGCGATTAACAGAAAAGGAAGATGAATCACTGCCAATAGATACAGTTCTTCAGACACTTCTGGCCTTTGC
AGTTACCTGTTATGGTATAGTTCATATTGCAGGGGAGTTTAAAGACATGGATGCCACTTCAGAACTAAAAAATAAGACAT
TTGACACACTAAGGAATCACCCATCATTTTATGTATTTAATCATCGTGGTCGAGTACTGTTCCGGCCTTCGGATACAACA
AATTCTTCAAACCAAGATGTATTGTCCTCTAACACATCACTGAAGTTACGAAAACTTGAATCACTGCATCGT

Alignment

ORF - retro_btau_1566 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.12 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRG
          RSYMRLTEKEDESLPID.VLQTLLAFAVTCYGIVHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRG
Retrocopy RSYMRLTEKEDESLPIDTVLQTLLAFAVTCYGIVHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRG

Parental  RVLFRPSDTTNSSNQDALSSNTSLKLRKLESLRR
          RVLFRPSDTTNSSNQD.LSSNTSLKLRKLESL.R
Retrocopy RVLFRPSDTTNSSNQDVLSSNTSLKLRKLESLHR

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	0.07 RPM	2.31 RPM
ERP005899_muscle	0.00 RPM	3.96 RPM
SRP017611_brain	0.32 RPM	3.24 RPM
SRP017611_kidney	0.30 RPM	5.63 RPM
SRP017611_liver	0.15 RPM	3.62 RPM
SRP030211_testis	0.58 RPM	4.50 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1566 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566 , retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,