RetrogeneDB ID: retro_sscr_42

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:5842926..5843880(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000014750
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000028933
• Aliases: None
• Description: None

Sequence

>retro_sscr_42
ATGACAATCCTGTATAATAGCAGCCTCCAAAAAGCCACCTTCTTCCTGACGGGCTTCCGAGGTCTGGAAGGTCTCCATGG
ATGGATCTCTCTTCCCTTCTGCTCCATCTATCTGGCAGTTATCGTAGGAAACCTCACCGTCCTCCACGTCATCCGTACCG
ATGTCACCCTCCACGAACCCATGTACTATTTCTTGGCCATGCTGGCCCTCACTGACCTGGGCCTTTGCCTTTCTACACTA
CCCACTGTGATGGGCATCTTCTGGTTTGGTGCCAGAGAAATCGGTATCCCTGCCTGCTTCACTCAGCTCTTCTTCATCCA
CACCTTGTCCCTCGTGGAGTCTTCAGTTCTCTTGTCCATGTCCGTTGACCGCTATGTGGCCATCTGCCACCCACTGCGTT
ACTCCACAGTCTTGACACCTGCGCGTATTGTCAGGATGGGACTGAGCTCGGTGCTTAGAAGTGCATTGCTCATCCTCCCC
CTGCCGTTTCTCCTTAAGCGCTTCCAGTACTGCCGCTCCCATGTGTTGGCCCATGCCTACTGTCTGCACCTGGAGATCAT
GAAGCTGGCCTGCTCTAGCATCACTGTCAATCACATCTACGGGCTCTTTGTTGTGGCCTGCACTGTAGGTGTGGACTCCC
TGCTCATCTTCCTCTCCTACGCCCTCATTCTCCGCACAGTCCTGGGCATTGCCTCCCGCCAGGAGCGCCTCCGCGCCCTC
AGCACCTGTGTCTCCCACATCTGCGCGGTGCTTCTCTTCTACATGCCCATGATTGGCTTGTCGCTTGTGCACCGCTTCGG
TGAACACCTGCCCCGCCTTGTGCACCTCCTCATGTCCTATGTGTATCTGCTGGTCCCCCCGCTCATGAACCCCATTGTTT
ACAGCATCAAGACCAAGCAGATCCGCCAACGCATCGCTAAGAAATTTCAGTTTATAAAATCGCTCAAGTGTTTT

Alignment

ORF - retro_sscr_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.84 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTILYNSSLQKATFFLTGFRGLEGLHGWISLPFCSIYLAVIVGNLTVLHVIRTDVTLHEPMYYFLAMLAL
          MTILYNSSLQKATFFLTGFRGLEGLHGWISLPFCSIYLAVIVGNLTVLHVIRTDVTLHEPMYYFLAMLAL
Retrocopy MTILYNSSLQKATFFLTGFRGLEGLHGWISLPFCSIYLAVIVGNLTVLHVIRTDVTLHEPMYYFLAMLAL

Parental  TDLGLCLSTLPTVMGIFWFGAREIGIPACFTQLFFIHTLSLVESSVLLSMSVDRYVAICHPLRYSTVLTP
          TDLGLCLSTLPTVMGIFWFGAREIGIPACFTQLFFIHTLSLVESSVLLSMSVDRYVAICHPLRYSTVLTP
Retrocopy TDLGLCLSTLPTVMGIFWFGAREIGIPACFTQLFFIHTLSLVESSVLLSMSVDRYVAICHPLRYSTVLTP

Parental  ARIVRMGLSSVLRSALLILPLPFLLKRFQYCRSHVLAHAYCLHLEIMKLACSSITVNHIYGLFVVACTVG
          ARIVRMGLSSVLRSALLILPLPFLLKRFQYCRSHVLAHAYCLHLEIMKLACSSITVNHIYGLFVVACTVG
Retrocopy ARIVRMGLSSVLRSALLILPLPFLLKRFQYCRSHVLAHAYCLHLEIMKLACSSITVNHIYGLFVVACTVG

Parental  VDLLLILLSYVLILCSVLSIASRTQRLKALNTCVAHICAVLLFYIPMIGLSVIHRFGKQAPHLVQVVMGF
          VD.LLI.LSY.LIL..VL.IASR..RL.AL.TCV.HICAVLLFY.PMIGLS..HRFG...P.LV...M..
Retrocopy VDSLLIFLSYALILRTVLGIASRQERLRALSTCVSHICAVLLFYMPMIGLSLVHRFGEHLPRLVHLLMSY

Parental  VYL----XMNPIVYSVKTKQIRDRV
          VYL.....MNPIVYS.KTKQIR.R.
Retrocopy VYLLVPPLMNPIVYSIKTKQIRQRI

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	0.29 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_42 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_42 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_42 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000028933	2 retrocopies	retro_sscr_21, retro_sscr_42 ,