RetrogeneDB ID: retro_sscr_415

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:56647182..56647740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000009290
• Aliases: None
• Description: None

Sequence

>retro_sscr_415
AATCTTCTCCATGAAATGGAACATACTGTACATTCTATGCTGGGATGTACTTATTACCAACATGTCAATTGGACCAGATA
TCCAACTGATTTTGCTGAGGTTTCTTTTATACCACTGGAGTATTTTGTGAACTATTATCTAGTGATTAACCAATTTGCCA
GACATCATCAAACGGGGAAGCCATGCTGAAAGATATGTATCATCTTTGTGGATTTAAAAAGACTTGTGCTGAAGTTGATA
GGCAACTTCAGCTCTTTTATGCCACTCTGGATTGTCTGCCATGGAAGCATCCCCTGAGAAGGTCAACCCCAGATATCCTC
AGGGAAGTGCAGAGTAAAGTTTATGGCTTACCAAACATTACAAATACTGCCCACTGCTGTGATTCAGCCACCTTGTGGGC
CATGGTGCCAAATATTACTCCTATCTGGTGTCCAGGACACTAACTTCTATGGTTTGGAAGGAAGGTATTCTACAGAATCC
TAATAACAGGCTACAGGTAAGTACCATTATATGGGGATGCTATCACATGTTAAGAGCAAAGAGCCAATTTTCATGATT

Alignment

ORF - retro_sscr_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.21 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NLFHEMGHAMHSMLGRTRYQHVTGTRCPTDFAEVPSILMEYFAADYRVVQQFARHYQTG-QSLPRSMVSR
          NL.HEM.H..HSMLG.T.YQHV..TR.PTDFAEV..I..EYF...Y.V..QFARH.QTG.......M...
Retrocopy NLLHEMEHTVHSMLGCTYYQHVNWTRYPTDFAEVSFIPLEYFVNYYLVINQFARHHQTG<EAMLKDMY-H

Parental  LCESKKVCAAADMQLQVFYAALDQLYHGPHPRGRCTTDVLRATQERFYGLPYVPGTAW-QLRFSHLVGYG
          LC..KK.CA..D.QLQ.FYA.LD.L....HP..R.T.D.LR..Q...YGLP....TA...L.FSHLVG.G
Retrocopy LCGFKKTCAEVDRQLQLFYATLDCL-PWKHPLRRSTPDILREVQSKVYGLPNITNTAH<LL*FSHLVGHG

Parental  AKYYSYLMSRAVASMVWRECFLQDPFNR-AAGERYRREMLAHGGGKEPLLMV
          AKYYSYL.SR...SMVW.E..LQ.P.NR.A.G......ML.H...KEP..M.
Retrocopy AKYYSYLVSRTLTSMVWKEGILQNPNNR<ATGKYHYMGMLSHVKSKEPIFMI

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	22.56 RPM
SRP014902_testis	0.00 RPM	30.27 RPM
SRP018288_heart	0.00 RPM	14.96 RPM
SRP018288_kidney	0.00 RPM	21.57 RPM
SRP018288_liver	0.00 RPM	7.84 RPM
SRP018288_lung	0.00 RPM	11.51 RPM
SRP018856_adipose	0.00 RPM	13.69 RPM
SRP035408_brain	0.00 RPM	8.70 RPM
SRP035408_liver	0.00 RPM	12.42 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_415 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_415 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000027001	1 retrocopy	retro_hsap_3891,
Gorilla gorilla	ENSGGOG00000009424	1 retrocopy	retro_ggor_2619,
Macaca mulatta	ENSMMUG00000006942	1 retrocopy	retro_mmul_1732,
Nomascus leucogenys	ENSNLEG00000013401	1 retrocopy	retro_nleu_1131,
Pongo abelii	ENSPPYG00000005207	1 retrocopy	retro_pabe_3172,
Sus scrofa	ENSSSCG00000009290	1 retrocopy	retro_sscr_415 ,