RetrogeneDB ID: retro_sscr_908

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:75900196..75900565(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMGT1
• Ensembl ID: ENSSSCG00000025854
• Aliases: None
• Description: membrane magnesium transporter 1 [Source:HGNC Symbol;Acc:28100]

Sequence

>retro_sscr_908
TGGCCCCATCTCTGTGGAAGAGGCTGTTGGGCCCTAGCCCAAGAGGCCTTTTCCTCTGCACAGCATCGTTCTTATATGTG
ATTAACAGAAAAGGAAGATGAATCACTGCCAATAGATATAGTTCTTCAGACACTTCTGGCCTTTGCAGTTACCATTTTTG
GTATAGTTCATATTGTGGAGGAGTTTAAAGACATGGATGCCACTTCAGAACTAAAAAATAAGGCATTTGACACATTGAAG
AATCACCTATCATTTTATGTATTTAATCATCGTGGTCAAGTACTGGTCCAGACTTTGGATACAGCAAATTCTTCAAACCA
AGATGCATTGTCCTCTAACACATTGAAATTACAAAAACTTGAATCACTG

Alignment

ORF - retro_sscr_908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.03 %
• Parental protein coverage: 94.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDMDATSE
          W..L.G.G..ALA..AFS.AQHRSYM.LTEKEDESLPIDIVLQTLLAFAVT..GIVHI..EFKDMDATSE
Retrocopy WPHLCGRGCWALAQEAFSSAQHRSYM*LTEKEDESLPIDIVLQTLLAFAVTIFGIVHIVEEFKDMDATSE

Parental  LKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTTNASNQDALSSNTSLKLRKLESL
          LKNK.FDTL.NH.SFYVFNHRG.VL....DT.N.SNQDALSSNT.LKL.KLESL
Retrocopy LKNKAFDTLKNHLSFYVFNHRGQVLVQTLDTANSSNQDALSSNT-LKLQKLESL

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
SRP014902_placenta	0.00 RPM	7.57 RPM
SRP014902_testis	0.00 RPM	14.71 RPM
SRP018288_heart	0.00 RPM	20.30 RPM
SRP018288_kidney	0.00 RPM	35.07 RPM
SRP018288_liver	0.00 RPM	14.07 RPM
SRP018288_lung	0.00 RPM	19.45 RPM
SRP018856_adipose	0.00 RPM	14.70 RPM
SRP035408_brain	0.00 RPM	12.35 RPM
SRP035408_liver	0.00 RPM	9.39 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_908 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_908 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,