RetrogeneDB ID: retro_sscr_653

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:155422129..155422745(+)
• Located in intron of: ENSSSCG00000014420

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000004465
• Aliases: None
• Description: Sus scrofa branched chain keto acid dehydrogenase E1, beta polypeptide (BCKDHB), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001123219]

Sequence

>retro_sscr_653
AGCCTTAAGAGGGCACCAACAAGGGCCTTGGATAACTCAGTGGCCAAAGATCCTACTGCAGTCACGTTTGGTGAGGATGT
GGCCTTTGGTGGAGTCTGATGTACCATTGGCTTGCGAGCCACATATGGTAAAGATGGAGTTTCTGATGCCCCCTCGTGTG
AACAAGGAGTTGCTGGATTGGAGTTTCGGTCACCGGGGCTACGGCCACTGCGGAAACTCGGCTTGCAGATTATATTTTCC
TGCTCTTGATCAGATTGTTAATGAAGCTGCAAAGCGTCCTGGCCGCTCTGGGGATCTCTTCAATTGTGGAAGCCTCACCG
TCCAGTCCCCTCAGAGCTGAGTCCACCATGGGGCTCTCTGTCATCCCCAGAGTCCTGAAATTTTTTTGCCTACTGCCCAG
GAGTCAAGGTGGTTGTACCCAGAAGCCCTTTCCAGGTTGAGGGACTTCTTTTGTCATGCACTGAAGATAAAAATCCTTGG
ATATTTTTTGAACCTAAGATACTTGACAGAGCAGCAGTGAAACAGGGTTCCCACCAAGCCACCATACAGCATTCTTCTGC
CCCAGGCTGAAGTCACCCAAGAAGGAGGTGATATCACTCCTGCTGCCTGGGGCACG

Alignment

ORF - retro_sscr_653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.48 %
• Parental protein coverage: 73.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NLFQAVTSALDNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVFNTPLCEQGIVG-FGIGIAVTG
          .L..A.T.ALDNS.AKDPTAV.FGEDVAFGGV..CT.GLR..YGKD.V...P.CEQG..G..G.....TG
Retrocopy SLKRAPTRALDNSVAKDPTAVTFGEDVAFGGV-*CTIGLRATYGKDGVSDAPSCEQGVAG<IGVSV--TG

Parental  ATAIAEIQFADYI-FPAFDQIVNEAAKYRYRSGDLFNCGSLTIRSPWGCVGHGALYHSQSPEA-FFAHCP
          ATA.AE...ADYI.FPA.DQIVNEAAK...RSGDLFNCGSLT..SP...V.HGAL.H.QSPE..FFA.CP
Retrocopy ATATAETRLADYI<FPALDQIVNEAAKRPGRSGDLFNCGSLTVQSPQS*VHHGALCHPQSPEI<FFAYCP

Parental  GIKVVVPRSPFQAKGLLLSCIEDKNPCIFFEPKILYRAAVEQ-VPIE-PYTIPLSQAEVIQEGSDVTLVA
          G.KVVVPRSPFQ..GLLLSC.EDKNP.IFFEPKIL.RAAV.Q.VP...PY.I.L.QAEV.QEG.D.T..A
Retrocopy GVKVVVPRSPFQVEGLLLSCTEDKNPWIFFEPKILDRAAVKQ>VPTKPPYSILLPQAEVTQEGGDITPAA

Parental  WGT
          WGT
Retrocopy WGT

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	0.93 RPM
SRP014902_testis	0.00 RPM	52.05 RPM
SRP018288_heart	0.00 RPM	16.79 RPM
SRP018288_kidney	0.00 RPM	41.47 RPM
SRP018288_liver	0.00 RPM	31.82 RPM
SRP018288_lung	0.00 RPM	2.65 RPM
SRP018856_adipose	0.00 RPM	3.75 RPM
SRP035408_brain	0.10 RPM	5.27 RPM
SRP035408_liver	0.00 RPM	48.58 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_653 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_653 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
Otolemur garnettii	ENSOGAG00000000645	1 retrocopy	retro_ogar_1111,
Sus scrofa	ENSSSCG00000004465	1 retrocopy	retro_sscr_653 ,
Tarsius syrichta	ENSTSYG00000006573	1 retrocopy	retro_tsyr_1006,