RetrogeneDB ID: retro_sscr_238

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:6431235..6431631(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000024720
• Aliases: None
• Description: None

Sequence

>retro_sscr_238
CTCTGCGAGAAGACCATGGAGCTGGTCCCCGAGCTGCACCACGAGGCTGAGGGACAGGTGCCAGCCTTCCGTGAGGACGG
ACTCAGGCAAGTTCTGGAGGAGAGGAAAGCTTTATAGGAACAAAACCAGTCTGATGTGAATGAAGCCAAGTCAGGTGGAC
GAAGTGATCTGATACCAACCACCAAGTTTCGAGACGGTCCTTTGTGAAGAAACCAGCGCTGCACGGCGGCACATCTGTAC
GACCGACTGCTCTGGATTAGAGCACTCAGGTGGGAGGATGGCAGTGCCTTGCCAAAGGCTTTACGATTTCACGTATGTGC
TGAAGAAACGGATTGGTTCAATCATTACGAAAACTCCCTTGCTACCCACACGAGGCCATCGGGAGGAGAGGAAGGC

Alignment

ORF - retro_sscr_238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 67.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LCEKAMELVRELHRAAEGQLPAFNEDGLRQVLEEMKALYEQNQSDVNEAKSGGRSDLIPTIKFRHCSLLR
          LCEK.MELV.ELH..AEGQ.PAF.EDGLRQVLEE.KAL.EQNQSDVNEAKSGGRSDLIPT.KFR...L.R
Retrocopy LCEKTMELVPELHHEAEGQVPAFREDGLRQVLEERKAL*EQNQSDVNEAKSGGRSDLIPTTKFRDGPL*R

Parental  NQRCTIAYLYDRLLRIRALRWEYGSVLPNALRFHMSAEEMDWFNHYKKSLATYMRSLGGDEG
          NQRCT.A.LYDRLL.IRALRWE.GS.LP.ALRFH..AEE.DWFNHY..SLAT..R..GG.EG
Retrocopy NQRCTAAHLYDRLLWIRALRWEDGSALPKALRFHVCAEETDWFNHYENSLATHTRPSGGEEG

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_238 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_238 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
Echinops telfairi	ENSETEG00000002718	1 retrocopy	retro_etel_1594,
Macropus eugenii	ENSMEUG00000016481	1 retrocopy	retro_meug_1309,
Monodelphis domestica	ENSMODG00000006443	1 retrocopy	retro_mdom_1191,
Rattus norvegicus	ENSRNOG00000008091	1 retrocopy	retro_rnor_2888,
Sarcophilus harrisii	ENSSHAG00000017422	1 retrocopy	retro_shar_343,
Sus scrofa	ENSSSCG00000024720	1 retrocopy	retro_sscr_238 ,