RetrogeneDB ID: retro_sscr_775

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:40961959..40962250(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSSSCG00000004912
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_sscr_775
GTCGTTTTTAAAGCTGAAGGACTAGACATTCCAATAGTTCATGGAGTGATCAAAGTTCATGAAAAAAATAATGGAGACAT
CAAATTTCTAACTGAAGGAGATAATAATGAAGTTGATGATAGAAGTTTGTACAAAGAAGGCCAGAACTGGCTCAAAAAGG
ACATGGTGGAAAGATCGAAAATGTTTTCATCATATGTTGGTATCGTCACCATAATAATGAATGACTATCCAAAATTCAAG
TATGCTCTTTTGGCTGCAATGGGTGCACATGTGTTACTAAAACATGAATCC

Alignment

ORF - retro_sscr_775 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 51.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLYKEGQNWLEKKDVVGRARGFLPYVGMV
          VVFK.EG.DIPIVH.VIKVHEK.NGDIKFLT.GDNNEVDDR.LYKEGQNWL.KKD.V.R...F..YVG.V
Retrocopy VVFKAEGLDIPIVHGVIKVHEKNNGDIKFLTEGDNNEVDDRSLYKEGQNWL-KKDMVERSKMFSSYVGIV

Parental  TIIMNDYPKFKYALLAVMGAYVLLKRES
          TIIMNDYPKFKYALLA.MGA.VLLK.ES
Retrocopy TIIMNDYPKFKYALLAAMGAHVLLKHES

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	21.24 RPM
SRP014902_testis	0.00 RPM	52.34 RPM
SRP018288_heart	0.00 RPM	26.40 RPM
SRP018288_kidney	0.00 RPM	59.99 RPM
SRP018288_liver	0.00 RPM	81.23 RPM
SRP018288_lung	0.10 RPM	37.47 RPM
SRP018856_adipose	0.00 RPM	21.30 RPM
SRP035408_brain	0.00 RPM	118.31 RPM
SRP035408_liver	0.00 RPM	207.11 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_775 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_775 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_1009

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775 ,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,