RetrogeneDB ID: retro_sscr_348

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:161942965..161943373(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000011945
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5G1
• Ensembl ID: ENSSSCG00000017544
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) [Source:HGNC Symbol;Acc:841]

Sequence

>retro_sscr_348
ATGCAGACCACTGGGGCACTACTCATTTCTCCTGCTCTGCTCCGCTCTTGTACCAGGGGTCTGATCAGGCCTGTGTCTGC
CTCCTTCCTGAGTAGGCCAGAAATCCCATCTGAACAGCCTCCCTGCAGCAGTGTCCCACTCCAGGTGGCCAGGCGGGAGT
TCCAGACCAGTGTTGTCTCCCAGGACATTGACACAGCGGCCAAGTTTATTGGTGCTGGGGCCGCCACAGTTGGTGTGGCT
GGTTCCGGGGCTGGCATTGGGACAGTGTTTGGCAGCTTGATCATTGGCTATGCCAGGAACCTGTCTCTGAAGCAGCAGCT
CTTCTCCTGTGCCATTCTGGGCTTTGCCCTGTCTGAGGCCATGGAGCTCTTCTGTTTGATGGTCGCCTTCCTTATCCTCT
TAGCCATG

Alignment

ORF - retro_sscr_348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTTGALLISPALLRSCTRGLIRPVSASFLSRPEIPSEQPPCSSVPLQVARREFQTSVVSRDIDTAAKFI
          MQTTGALLISPALLRSCTRGLIRPVSASFLSRPEIPSEQPPCSSVPLQVARREFQTSVVS.DIDTAAKFI
Retrocopy MQTTGALLISPALLRSCTRGLIRPVSASFLSRPEIPSEQPPCSSVPLQVARREFQTSVVSQDIDTAAKFI

Parental  GAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
          GAGAATVGVAGSGAGIGTVFGSLIIGYARN.SLKQQLFS.AILGFALSEAM.LFCLMVAFLIL.AM
Retrocopy GAGAATVGVAGSGAGIGTVFGSLIIGYARNLSLKQQLFSCAILGFALSEAMELFCLMVAFLILLAM

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	47.92 RPM
SRP014902_testis	0.14 RPM	42.58 RPM
SRP018288_heart	0.31 RPM	338.87 RPM
SRP018288_kidney	0.30 RPM	154.95 RPM
SRP018288_liver	0.00 RPM	74.68 RPM
SRP018288_lung	0.00 RPM	15.78 RPM
SRP018856_adipose	0.12 RPM	61.78 RPM
SRP035408_brain	1.52 RPM	27.79 RPM
SRP035408_liver	2.32 RPM	17.79 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_348 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006341	1 retrocopy	retro_acar_9,
Bos taurus	ENSBTAG00000018339	3 retrocopies	retro_btau_1506, retro_btau_423, retro_btau_431,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550,
Macropus eugenii	ENSMEUG00000005744	2 retrocopies	retro_meug_1650, retro_meug_1973,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Oryctolagus cuniculus	ENSOCUG00000016225	2 retrocopies	retro_ocun_346, retro_ocun_375,
Otolemur garnettii	ENSOGAG00000011713	3 retrocopies	retro_ogar_1847, retro_ogar_2767, retro_ogar_531,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Sus scrofa	ENSSSCG00000017544	1 retrocopy	retro_sscr_348 ,
Tursiops truncatus	ENSTTRG00000008526	1 retrocopy	retro_ttru_279,
Vicugna pacos	ENSVPAG00000007653	1 retrocopy	retro_vpac_282,