RetrogeneDB ID: retro_ocun_660

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:98972403..98972796(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008927
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMGT1
• Ensembl ID: ENSOCUG00000029505
• Aliases: None
• Description: membrane magnesium transporter 1 [Source:HGNC Symbol;Acc:28100]

Sequence

>retro_ocun_660
ATGGCGCCGTCGCTGTGGAAGGGGCTGGTAGGCATCGGCCTCTTTGCTCTAGCCCACGCCGCCTTTTCCGCTGCTCAGCA
TCGTTCTTATATGCGATTGACAGAAAAGGAAGAGGAATCACTGCCAACAGATATAGTGCTTCAGACACTTCTGGCCTTTG
CAGTTACCTGTTATGGTACAGTTCATATTGCAGGGGAATTTAAAAACATGGACGCTACTTCCGAACTAAAGAATAAGACA
TTTGATACGTTAAGGAATCACCCATCCTTTTATGTCTTTAACCATCGCGGTCGAGTACTGTTCCGGCCTTCAGATCCAAG
AAATTCTTCAAATCAAGATGCGTTGTCCTCTAACACATCGGTGAAGTTACGAAAACTTGAGTCGCTGCGCCGT

Alignment

ORF - retro_ocun_660 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDM
          MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKE.ESLP.DIVLQTLLAFAVTCYG.VHIAGEFK.M
Retrocopy MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEEESLPTDIVLQTLLAFAVTCYGTVHIAGEFKNM

Parental  DATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTTNSSNQDALSSNTSLKLRKLESLRR
          DATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSD..NSSNQDALSSNTS.KLRKLESLRR
Retrocopy DATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDPRNSSNQDALSSNTSVKLRKLESLRR

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	0.00 RPM	38.36 RPM
SRP017611_kidney	0.00 RPM	48.35 RPM
SRP017611_liver	0.00 RPM	8.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_660 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_660 has 0 orthologous retrocopies within eutheria group .

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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,