RetrogeneDB ID: retro_sscr_142

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:274911760..274912400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH1
• Ensembl ID: ENSSSCG00000001922
• Aliases: None
• Description: ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila) [Source:HGNC Symbol;Acc:689]

Sequence

>retro_sscr_142
TATTTCACTGGCCTTGAATGTGGACATAAGTTTTGTATGTAGTGGTGGAGCAAATATTTAACTACCAAAATAATGGAAGA
AGGAATGGGACAGACTATTTCGTGTCCTGCTCATGGTTGTGATATTTTAGTGGATGACAATACAGTTAAGCAACTGATCA
CTGATTCAGAAGTTGAATTAAAGCATTTAGCATTTAATAACAAACAGCTTTGTAGAGTGCAATCAACTGTTAAAGTGGTG
TCCTGCCCCAGATTGCCATCATGTTGTGAAAGTTCAATATTCTGATGCTAAACATGATCGCTGAAAATGTGGGTGCCAGT
TTTGCTTTAAGTATGGAGAAAATTGGCATGACCCTGTTAAGTGTAAATGGTTGAATAAGTGGATTAAAAAGTGTGATGAT
GACAGTGAAACTTCTAATTGGATTGCAGCTAACACAAAGGAATGTCCCAAATGCCACGTCACAATTGAGAAAGATGGCAG
TTGTAATCACATGATCTGTAGTAACCAGAACTGTAAAGCAAAGTTTTGCTGGTTGTATCTTGGTCCTTGAGAACCACATC
GATCTGCTTGGTACAACTGTAACTGCTATAATGAGGATGATGCAAAGGCAGCAAGAGACAAAGGCAGCAAGGATGATGCA

Alignment

ORF - retro_sscr_142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 62.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQ-HLITNS
          YFTGLECGHKFCM..WS.YLTTKIMEEGMGQTISCPAHGCDILVDDNTV..LITDS.V.LK...HLITNS
Retrocopy YFTGLECGHKFCM*WWSKYLTTKIMEEGMGQTISCPAHGCDILVDDNTVKQLITDSEVELKHL>HLITNS

Parental  FVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSN
          FVECN.LLKWCPAPDCHHVVKVQY.DAK..R.KCG.QFCF..GENWHDPVKCKWL.KWIKKCDDDSETSN
Retrocopy FVECNQLLKWCPAPDCHHVVKVQYSDAKHDR*KCGCQFCFKYGENWHDPVKCKWLNKWIKKCDDDSETSN

Parental  WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQE
          WIAANTKECPKCHVTIEKDG.CNHM.C.NQNCKA.FCW..LGP.EPH.SAWYNCN.YNEDDAKAARD...
Retrocopy WIAANTKECPKCHVTIEKDGSCNHMICSNQNCKAKFCWLYLGP*EPHRSAWYNCNCYNEDDAKAARDKGS

Parental  RSRA
          ...A
Retrocopy KDDA

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	10.35 RPM
SRP014902_testis	0.00 RPM	19.80 RPM
SRP018288_heart	0.10 RPM	30.52 RPM
SRP018288_kidney	0.10 RPM	19.01 RPM
SRP018288_liver	0.00 RPM	15.83 RPM
SRP018288_lung	0.31 RPM	13.95 RPM
SRP018856_adipose	0.00 RPM	27.31 RPM
SRP035408_brain	0.00 RPM	14.13 RPM
SRP035408_liver	0.00 RPM	15.24 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_142 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_142 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000012095	1 retrocopy	retro_ogar_3490,
Sus scrofa	ENSSSCG00000001922	2 retrocopies	retro_sscr_142 , retro_sscr_200,
Drosophila melanogaster	FBgn0017418	1 retrocopy	retro_dmel_25,