RetrogeneDB ID: retro_sscr_195

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:255025357..255026233(-)
• Located in intron of: ENSSSCG00000005272

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSSSCG00000002956
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_sscr_195
TTTGCCACATCACGGAAGATGGCAGTCACAACAGTGAACGAGGTGGCGGGTGGCTCGAGCTGGGGGCCTGCAGTGGCCTT
GGGCCCAGTCCTGCAGGCCGCAGCCGGCATGTACGAACAACTCAAGGGCAAGTGGAACCATGAAAGCCCCAATCTTAGCA
AATGCAGTGAAGAACTGGGCCGTCTCAAGCTGGTTCTGTTGGAGCTCAACTTCCTGCCAACCACAGGGACCAAACTGACC
AAACAGCAGCTCATTCTGCCCCATGACATACTAGAGATTGGGGCCCAGTGGAGTAGCTTACACAAGGACATCCCCTCCTT
TTAGCGGTACATGGTCCAGCTCAAGTGTTGCTACTTTGATTACGAATAGCTCCCAGAGTCAGCCTATATGCACCAGCTCT
TGGGGCTCAACCTCGTCTTCCTGCTGTCTCAGCACCAGGTAGCTGAGTTCCACACAGAGCTGGAGTGGCCACCTGCCAAG
GACATCCAGACCAATGTATACATCAAGCAGCCGGTGTCCCTGGAGCAATACCTGATGGAGGGCAGCTACAATAAGGTGTT
CCTGGCCAAAGGAAACATCCCTGTAGAGAGCTGTACATTCTTCATTGACATCCTGTTTGACACTATCAGGGACGAGATTG
CTGGCTGCATCGAGAAGGCCTATGAAAAAATCCTCCTCACTGAGGCCACTCGGATCCTCTTCTTCAACACACCCAAAAAG
ATGACGGACTATGCCAGGAAGCGAGGGTGGATCCTGGGCCTCAACAACTACTACAGCTTTGTCAGCCAGCAGCAGAACCC
AGAAGAAACCACCATCTCCTCTTCAGAGCTGGCCAAACAGGTCATCAAGTACACCTGGCAGCTGGAGATGATTGTC

Alignment

ORF - retro_sscr_195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 83.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAASRKMAAATVNGVAGGSSSGPAAASGAVLQAAAGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELN
          FA.SRKMA..TVN.VAGGSS.GPA.A.G.VLQAAAGMYEQLKG.WN..SPNLSKC.EELGRLKLVLLELN
Retrocopy FATSRKMAVTTVNEVAGGSSWGPAVALGPVLQAAAGMYEQLKGKWNHESPNLSKCSEELGRLKLVLLELN

Parental  FLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLL
          FLPTTGTKLTKQQLIL..DILEIGAQWS.L.KDIPSF.RYM.QLKC.YFDY.E.LPESAYMHQLLGLNL.
Retrocopy FLPTTGTKLTKQQLILPHDILEIGAQWSSLHKDIPSF*RYMVQLKCCYFDY-E*LPESAYMHQLLGLNLV

Parental  FLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTI
          FLLSQ..VAEFHTELE..PAKDIQTNVYIK.PVSLEQYLMEGSYNKVFLAKGNIP.ES.TFFIDIL.DTI
Retrocopy FLLSQHQVAEFHTELEWPPAKDIQTNVYIKQPVSLEQYLMEGSYNKVFLAKGNIPVESCTFFIDILFDTI

Parental  RDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRGWVLGLNNYYSFASQQQKPEDTTIPSTELAK
          RDEIAGCIEKAYEKIL.TEATRILFFNTPKKMTDYA.KRGW.LGLNNYYSF.SQQQ.PE.TTI.S.ELAK
Retrocopy RDEIAGCIEKAYEKILLTEATRILFFNTPKKMTDYARKRGWILGLNNYYSFVSQQQNPEETTISSSELAK

Parental  QVIEYARQLEMIV
          QVI.Y..QLEMIV
Retrocopy QVIKYTWQLEMIV

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	104.99 RPM
SRP014902_testis	0.14 RPM	60.40 RPM
SRP018288_heart	0.03 RPM	46.76 RPM
SRP018288_kidney	0.20 RPM	81.86 RPM
SRP018288_liver	0.32 RPM	98.66 RPM
SRP018288_lung	0.00 RPM	69.45 RPM
SRP018856_adipose	0.17 RPM	73.63 RPM
SRP035408_brain	0.00 RPM	85.53 RPM
SRP035408_liver	0.26 RPM	67.22 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_195 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005931	1 retrocopy	retro_cfam_2206,
Myotis lucifugus	ENSMLUG00000009902	2 retrocopies	retro_mluc_2137, retro_mluc_2480,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Sus scrofa	ENSSSCG00000002956	1 retrocopy	retro_sscr_195 ,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,