RetrogeneDB ID: retro_sscr_530

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:75345230..75345807(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADAL
• Ensembl ID: ENSSSCG00000004710
• Aliases: None
• Description: adenosine deaminase-like [Source:HGNC Symbol;Acc:31853]

Sequence

>retro_sscr_530
CAGGAGAACAAGAGCCAGAGGTCAATCTTTTACTTGGAATTATCTAAAGTGGAACTTCATACCCAGGTGAATGGATCGAT
CAGTTCTAATACTGTGAAAAAATGAAAAGCCAAAAAGCCAGGTCTTAAAATCCATGATCAGATGACTGATTAACAAAGGG
GAAAAAAAAGGACTTTAGAAGAATGTTTCCAGATATTTCAAATTATTTATAAGCTTTGCATTAGCCCTGAAGATATTTTA
ATGGACACAAAAGATGTCATTAAAGAATTCATAGATAATGATGTCAATACCTAAAGTAAGGAACACACACAGAAGAGAAA
ATGCTACAAGAATGACTAAAAAGACTTACAACGGAATCTGTGCTTGAGAAGATAAAACCATCTGAAAAAGGAACATAGAC
ATTGATGTTAGATATCGGATAGCAGTCGACAGAAGAGGTGACACTTCTGTTGCCAAGGAGACTATTAGACTTGCTAAAGA
GTTCTTCCTTTCTACTGAGGACGAAGTTCTTGGGCTCAACCTGGGTGGAGACCCTACTGTAGGAGAAGCAAAATTTCTTG
GAACATTTTTAGAAGCT

Alignment

ORF - retro_sscr_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.13 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEQQSWKTTFYSKLPKVELHAHLNGSISSNTIKKLITKKPGLKIHDQMTMIDKGKKRTLEECFQMFPIIH
          .E..S....FY..L.KVELH...NGSISSNT.KK...KKPGLKIHDQMT........TLEECFQ.F.II.
Retrocopy QENKSQRSIFYLELSKVELHTQVNGSISSNTVKK*KAKKPGLKIHDQMTD*QRXXXXTLEECFQIFQIIY

Parental  QLTTSPEDILMVTKDVIKEFADDGV-KYL-ELRSTPRGENATGMTKKTY-VESVLEGIKQSK-QENVDID
          .L..SPEDILM.TKDVIKEF.D..V..YL...R.T.R.ENAT.MTKKTY..ESVLE.IK.S....N.DID
Retrocopy KLCISPEDILMDTKDVIKEFIDNDV<QYL<KVRNTHRRENATRMTKKTY>TESVLEKIKPSE<KRNIDID

Parental  VRYLISIDRRGGPSAAKENVKLAEEFFLSTEGIVLGLDLSGDPTAGQAKDFLEPLLEA
          VRY.I..DRRG..S.AKE...LA.EFFLSTE..VLGL.L.GDPT.G.AK.FL...LEA
Retrocopy VRYRIAVDRRGDTSVAKETIRLAKEFFLSTEDEVLGLNLGGDPTVGEAK-FLGTFLEA

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	2.12 RPM
SRP014902_testis	0.00 RPM	4.95 RPM
SRP018288_heart	0.00 RPM	11.58 RPM
SRP018288_kidney	0.00 RPM	7.88 RPM
SRP018288_liver	0.00 RPM	4.48 RPM
SRP018288_lung	0.00 RPM	15.07 RPM
SRP018856_adipose	0.00 RPM	3.94 RPM
SRP035408_brain	0.00 RPM	6.57 RPM
SRP035408_liver	0.00 RPM	2.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_530 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_530 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1539

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014476	1 retrocopy	retro_btau_1539,
Cavia porcellus	ENSCPOG00000002337	1 retrocopy	retro_cpor_1193,
Oryctolagus cuniculus	ENSOCUG00000024818	2 retrocopies	retro_ocun_1237, retro_ocun_85,
Sus scrofa	ENSSSCG00000004710	1 retrocopy	retro_sscr_530 ,