RetrogeneDB ID: retro_sscr_1171

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:106562613..106562840(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000031018
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MINOS1
• Ensembl ID: ENSSSCG00000028414
• Aliases: None
• Description: mitochondrial inner membrane organizing system 1 [Source:HGNC Symbol;Acc:32068]

Sequence

>retro_sscr_1171
ATGTCGGATTCAGATCTCAGTAGGAAGTGGGACCGGTGCTTGGAGGATGAGGTCGTGAAGATAGGTACTGGTTTGGGATT
AAGACTTGTTTTCTCACTTCCTTCTTTAAAAGACGAATGTGGCCACTGGCCTTGGGTTCTGGAATGGGATTGGGAATGGC
CTACTCCAACTGTCAGCATGATTTCCAGGCTCTGTATCTACTACATAGAAAACACGTCAAAGAGCAG

Alignment

ORF - retro_sscr_1171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDSELGRKWDRCLADAVVKIGTGFGLGLVFSL-TFFKRRMWPLAFGSGMGLGMAYSNCQHDFQAPYLLH
          MSDS.L.RKWDRCL.D.VVKIGTG.GL.LVFSL..FFKRRMWPLA.GSGMGLGMAYSNCQHDFQA.YLLH
Retrocopy MSDSDLSRKWDRCLEDEVVKIGTGLGLRLVFSL<SFFKRRMWPLALGSGMGLGMAYSNCQHDFQALYLLH

Parental  GKYVKEQ
          .K.VKEQ
Retrocopy RKHVKEQ

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	32.25 RPM
SRP014902_testis	0.00 RPM	67.05 RPM
SRP018288_heart	0.00 RPM	90.18 RPM
SRP018288_kidney	0.00 RPM	98.21 RPM
SRP018288_liver	0.00 RPM	29.26 RPM
SRP018288_lung	0.00 RPM	44.80 RPM
SRP018856_adipose	0.00 RPM	136.33 RPM
SRP035408_brain	0.00 RPM	59.23 RPM
SRP035408_liver	0.00 RPM	46.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1171 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1171 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003110	3 retrocopies	retro_amel_1685, retro_amel_502, retro_amel_689,
Felis catus	ENSFCAG00000003066	2 retrocopies	retro_fcat_1448, retro_fcat_739,
Gallus gallus	ENSGALG00000004039	1 retrocopy	retro_ggal_19,
Loxodonta africana	ENSLAFG00000016199	1 retrocopy	retro_lafr_825,
Mus musculus	ENSMUSG00000050608	1 retrocopy	retro_mmus_2357,
Rattus norvegicus	ENSRNOG00000042696	2 retrocopies	retro_rnor_16, retro_rnor_2460,
Sus scrofa	ENSSSCG00000028414	1 retrocopy	retro_sscr_1171 ,
Tupaia belangeri	ENSTBEG00000004024	1 retrocopy	retro_tbel_4339,
Vicugna pacos	ENSVPAG00000011525	1 retrocopy	retro_vpac_607,