RetrogeneDB ID: retro_sscr_421

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:94666471..94666944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISOC1
• Ensembl ID: ENSSSCG00000014258
• Aliases: None
• Description: isochorismatase domain containing 1 [Source:HGNC Symbol;Acc:24254]

Sequence

>retro_sscr_421
CAAAGATTGTTGCAAGAGGCTCGGATTTTAGGAATTTTAGTTATTGTAACAGAGCAATATCCGAAAGTCTTGGAAGCACT
GTTCAGGAAATCGATTTAATAGGTGTAAAAGTCATACTTCGAAAGACCAAGTTTTCAATGGTATTACCAGAAGTAGAAGC
AGCAATAGCAGAGAGTCCTGGAGTCAGGAGTATTTTGTTATTCAGGGTAGGAGCTCGTGTGTACATCCAGCAAACAGCTC
TGGAGCTTGTTGGCCAAGGTATCAAGGTTCATACTGTTGTTGACACCATGTTGTCAAGAAGCATGATGGACAGGATGTTT
GCTCTTGAGCGTCTTGCTTGAACTGGGATCATAGTGATGACAAGTGAGGCCCTCCTGTTGCAGCTGGTGGCTGATAAAGA
CCATCCAAAATTCAAGGAAATTTAGAATCTAATTAAGGCAAGTTCTCCAGAGTCCGATCTGCTTTCCAAAGTA

Alignment

ORF - retro_sscr_421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.13 %
• Parental protein coverage: 53.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRLLQGARILGIPVIVTEQYPK-GLGSTVQEIDLTGVKLVLPKTKFSMVLPEVEAALAEIPGVRSVVLFG
          QRLLQ.ARILGI.VIVTEQYPK..LGSTVQEIDL.GVK..L.KTKFSMVLPEVEAA.AE.PGVRS..LF.
Retrocopy QRLLQEARILGILVIVTEQYPK<SLGSTVQEIDLIGVKVILRKTKFSMVLPEVEAAIAESPGVRSILLFR

Parental  VETHVCIQQTALELVGRGIEVHIVADATSSRSMMDRMFALERLARTGIIVTTSEAVLLQLVADKDHPKFK
          V...V.IQQTALELVG.GI.VH.V.D...SRSMMDRMFALERLA.TGIIV.TSEA.LLQLVADKDHPKFK
Retrocopy VGARVYIQQTALELVGQGIKVHTVVDTMLSRSMMDRMFALERLA*TGIIVMTSEALLLQLVADKDHPKFK

Parental  EIQNLIKASAPESGLLSKV
          EI.NLIKAS.PES.LLSKV
Retrocopy EI*NLIKASSPESDLLSKV

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	31.72 RPM
SRP014902_testis	0.00 RPM	25.04 RPM
SRP018288_heart	0.00 RPM	99.95 RPM
SRP018288_kidney	0.00 RPM	30.93 RPM
SRP018288_liver	0.00 RPM	69.24 RPM
SRP018288_lung	0.00 RPM	42.56 RPM
SRP018856_adipose	0.00 RPM	149.51 RPM
SRP035408_brain	0.00 RPM	19.76 RPM
SRP035408_liver	0.00 RPM	54.25 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_421 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_421 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_421 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006851	1 retrocopy	retro_chof_1203,
Oryctolagus cuniculus	ENSOCUG00000017498	1 retrocopy	retro_ocun_449,
Sus scrofa	ENSSSCG00000014258	2 retrocopies	retro_sscr_421 , retro_sscr_443,