RetrogeneDB ID: retro_sscr_1043

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:127459035..127459503(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000009052
• Aliases: None
• Description: None

Sequence

>retro_sscr_1043
GCACAGTGTGGGAAAATAAAGTGCACGATGAAGTCTTCAGACTATGTCATAAAATATGCTGGTGTCTACGGTACTGGCCT
TGCAATATGGGCGCAATCTGTGACTTTCTCTGAAGCTTGGGTTTGTCATGGTAGGAAGTGTCTCAGGACACATGCCTGTG
CCTGCCCACTTCCTGATGCTGAGTATGTGGAATGTGAATGGGGTATCTGGGACCATGGAGGGAGGATCTTCGGTTGTTCT
TTTTGACATAACTTTCTCTGTGAAGATGATCAGTTTGAACATCAAGACAGCTGCCAAGTTTTAGAGGTGGAAACATTTAG
ATGTGTTTCATGCAATCAGCTTGGTCAGCACTCCTGTCTCCGTTGTAAGGCTTGTTTCTGTGATGATCACACAAGGAGCA
AGGTGTTTAAACAAGAAAAAGGAAAACAGCCTCCCTGCCCGAAATATGGACATGAAACTCAGGAAACC

Alignment

ORF - retro_sscr_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 53.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AQCGKTKCMMKSSDCVIKHAGVYSTGLAM-VGAICDFC-EAWVCHGRKCLSTHACACPLTDAECVECERG
          AQCGK.KC.MKSSD.VIK.AGVY.TGLA...GAICDF..EAWVCHGRKCL.THACACPL.DAE.VECE.G
Retrocopy AQCGKIKCTMKSSDYVIKYAGVYGTGLAI<MGAICDFL>EAWVCHGRKCLRTHACACPLPDAEYVECEWG

Parental  VWDHGGRIFSCSFCHNFLCEDDQFEHQASCQVLEAETFKCVSCNRLGQHSCLRCKACFCDDHTRSKVFKQ
          .WDHGGRIF.CSF.HNFLCEDDQFEHQ.SCQVLE.ETF.CVSCN.LGQHSCLRCKACFCDDHTRSKVFKQ
Retrocopy IWDHGGRIFGCSF*HNFLCEDDQFEHQDSCQVLEVETFRCVSCNQLGQHSCLRCKACFCDDHTRSKVFKQ

Parental  EKGKQPPCPKCGHETQET
          EKGKQPPCPK.GHETQET
Retrocopy EKGKQPPCPKYGHETQET

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	7.17 RPM
SRP014902_testis	0.00 RPM	16.27 RPM
SRP018288_heart	0.00 RPM	14.83 RPM
SRP018288_kidney	0.00 RPM	31.42 RPM
SRP018288_liver	0.00 RPM	25.27 RPM
SRP018288_lung	0.31 RPM	10.49 RPM
SRP018856_adipose	0.00 RPM	31.42 RPM
SRP035408_brain	0.00 RPM	17.98 RPM
SRP035408_liver	0.00 RPM	35.11 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1043 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1043 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
Mus musculus	ENSMUSG00000031711	1 retrocopy	retro_mmus_344,
Oryctolagus cuniculus	ENSOCUG00000014580	1 retrocopy	retro_ocun_1479,
Sus scrofa	ENSSSCG00000009052	1 retrocopy	retro_sscr_1043 ,