RetrogeneDB ID: retro_rnor_689

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:48771641..48771996(+)
• Located in intron of: ENSRNOG00000046598

Retrocopy information

• Ensembl ID: ENSRNOG00000003214
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mmgt1
• Ensembl ID: ENSRNOG00000000881
• Aliases: None
• Description: Membrane magnesium transporter 1 [Source:UniProtKB/Swiss-Prot;Acc:B5DF51]

Sequence

>retro_rnor_689
ATGGTGGCGTGGCTGTGGAAGGTGCTGGTGGGCGTTGGTCTCTCCGCCCTCGCCCATGCTGCCTTTTCGGCTGCACAGCA
TCGTTCTCACATGAGGCTGGCAGAAATGAAGTATGAGCCGCTGCCGACCGATATAGTTCTTCAGACACTTTTGGCCTTTG
CCCTTACCCTGTATGGGCGTAGTTCATACTGCAGGGGACTTTAGAGACCGGGATGCCACTTCAGAACTAAAGAATGTGAC
ATTTGACACCTTAAGGAATCGCCCGTCTTTTTATGTGTTTCAACATTCTGGTTCCAGTCTTCTCCAGCCTTCGGATACAA
CTCGTTCTTCAAACCTCAACGTGCCATCTTCCGAT

Alignment

ORF - retro_rnor_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 90.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSLWKGLVGVGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVT-CYGIVHIAGEFKD
          M...LWK.LVGVGL.ALAHAAFSAAQHRS.MRL.E...E.LP.DIVLQTLLAFA.T.C.G.VH.AG.F.D
Retrocopy MVAWLWKVLVGVGLSALAHAAFSAAQHRSHMRLAEMKYEPLPTDIVLQTLLAFALT>CMGVVHTAGDFRD

Parental  MDATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDATNSSNLDALSSN
          .DATSELKN.TFDTLRN.PSFYVF.H.G..L..PSD.T.SSNL...SS.
Retrocopy RDATSELKNVTFDTLRNRPSFYVFQHSGSSLLQPSDTTRSSNLNVPSSD

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
SRP017611_brain	2.44 RPM	3.88 RPM
SRP017611_kidney	1.33 RPM	5.58 RPM
SRP017611_liver	0.87 RPM	3.77 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_689 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_689 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 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,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,