RetrogeneDB ID: retro_sscr_215

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:5595942..5596423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000028490
• Aliases: None
• Description: None

Sequence

>retro_sscr_215
ACAAACACCTTGAATGACCTTGGCCTTCACTGGAGGATGTGAATGACCCTGAATGTGGTGGCAGATGACTTTATCTTTGA
TGGGTCCTCTCTTCTTGCTCATATGCATGGATATGCATATGTAAGATGCTCTAGTTAGGGGAAAAAAAGTATGATAGTTC
CCATTCAGTTTATACATCAGCTGAGCAATGGAGTGGAAGACTGATAATCATAAATCATCTTCCTATTACGCTTCCTCTTA
TAGCATCCTAGGTTGAGTTCTCACTGGGAAGCCTCCACTTCGATATTCCCATTCAGGGTGCCATGTACTCCCCACAGTCA
AATCGGGTTTTCAGAGAAAGTGGCTGACAGGGTGAAAGGAATTCTTGCAGATCCCAACTTGTACTTCCTAGCTTTGACCT
TCTTTGTCACTGCATTTCATCTTTGTTTTGATTTCCTAACATTTAAAAAATGGCAACAGTTTCTGCAAGAAAAATAAGAG
C

Alignment

ORF - retro_sscr_215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.6 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNALDEPVSHWRPRLTLNVMVDDFVFDGAALPADVH--RYMKMVQLGKTVHYLPILFIDQLSNRVKD-LM
          .N.L.....HWR...TLNV..DDF.FDG..L.A..H...Y......GK.....PI.FI.QLSN.V.D.L.
Retrocopy TNTLNDLGLHWRM*MTLNVVADDFIFDGSSLLAHMHGYAYVRCSS*GKKSMIVPIQFIHQLSNGVED<LI

Parental  VINRSTAELPLTVSYDKISLGRLRFWIHMQDAVYSLQ-QLGFSEKDADEVKGIFVDTNLYFLALTFFVAA
          .IN.....LPL..S....SLG.L.F.I..Q.A.YS.Q.Q.GFSEK.AD.VKGI..D.NLYFLALTFFV.A
Retrocopy IINHLPITLPLIAS*VEFSLGSLHFDIPIQGAMYSPQ>QIGFSEKVADRVKGILADPNLYFLALTFFVTA

Parental  FHLLFDFLAF-KNDISFWKKKKT
          FHL.FDFL.F.KN..SF.KK.K.
Retrocopy FHLCFDFLTF>KNGNSFCKKNKS

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	85.48 RPM
SRP014902_testis	0.00 RPM	34.65 RPM
SRP018288_heart	0.00 RPM	9.67 RPM
SRP018288_kidney	0.00 RPM	41.57 RPM
SRP018288_liver	0.00 RPM	26.23 RPM
SRP018288_lung	0.00 RPM	34.42 RPM
SRP018856_adipose	0.00 RPM	23.35 RPM
SRP035408_brain	0.00 RPM	14.32 RPM
SRP035408_liver	0.00 RPM	20.58 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_215 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_215 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019472	1 retrocopy	retro_cjac_2519,
Equus caballus	ENSECAG00000013231	1 retrocopy	retro_ecab_371,
Sus scrofa	ENSSSCG00000028490	1 retrocopy	retro_sscr_215 ,