RetrogeneDB ID: retro_sscr_1118

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL895800.1:7695..9171(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PADI6
• Ensembl ID: ENSSSCG00000003484
• Aliases: None
• Description: None

Sequence

>retro_sscr_1118
AACCGCATCCCTATTAACATGAGCCAGCTCACAAAGGTGTTCTCTACAGGGGAAATAAAGAATCTGTCCCAGATAACACT
GAAAGTTCAGGGCCCAGCTGCATTTTAAAGAAACCCTGGCTCATTCTCCACATCCCCAGGGAAGAATCAGAGAAGGTGAG
AGTCTGCCAACCACAAAAAGACAACTCCAGCACCTTCAAATTGGTCTTGGGACCTGGCTAGCACACCTTACCTTTGCCCC
CCTTAAGGACAACTTGCAGGAAAACTTCTATGCCAAAGCCTTAGAGTTCCTGTCCACCAGATTCTTGGGACTGATTTCCT
AATCAGTCTCCCTGGTGGAAGAGTCTCAAGACCTGTCAATTCCAGAGATTCTGGCATACAAAGACTTGGTGGTATTCTGG
GTGACTCCTTGCATCTTTAGCCCCAGCACCTAGATGCCTTTAGAGGTATAGTGTGCAGAGAGCTGCAGGTCCAGGGCTCT
GTGAACACAGTGATGGAGCTTAGTGAGAGGAGTAACAGCTAGGTTGGCATCCACCTAGAGGACCTTAACCACTCAGGCAG
GTGGCAGCAGGATAATATGGTCTTCTGCTTCACCCAGGCTCCCACAAGACTATTTCCTTAGTCCTTGACACCTTCTACAT
CCCCAAGATAAACAATTTCCCCATGAAATACTGAGCCCTGGGTTGGCTACATGACCCAACACACCCAGAACCATAGAGAG
GCAAGTATAGATTCCATTGGGAACCTGATGGTGTCCCCACTCATCAAGGACAAAGGGAAAGAGTACCCTCTAGGCAGGAT
CCTCACTGACAACAGCTTTTACCCCAGCAAGAATGGTGGGGGACATGAGTAAGACCCCTGGGGATTTCCTCTATGCCCAG
CAAATCCAGGATCCTTTGGAACTCTTCTTGGACTGGTTGATGATTGGCCACACCCATGAACTCATGTGCTTGATCCCCAC
ATAGTACAAGGTAGAAGGCAAAAAGGACTTTTGGCTGCTTCTGGTCAGCCCAGCTCCTGCTACAGATTTTTTAAGGAGAA
ACAGAGGAGGGCTATGGAGATGTACCCTGTTTGGAAAGATTAGAAAAGAACAACTCCTTTCTAATAGGAGGGAGGCCAAT
ACTATCAATCAACTTCTGACTGATGAAAACCTGAGGAAGCATAACGACTATGTGGAGAAGCGCATCAACATGAATCGCGC
CATCCTGAAAAGGGAGCTGAGCCTGGTGGAGAAGGAAATCATGAACAACCCACAGCTCTTCTGCTTGGAACAAATTGACA
ATGCTCCTCCAACGAGCAGACCAGGAAACTCTTTGCAAACTCAGTTTCCGACCTGCTGCAGATAATTGTGATGGGCCAGA
ATCTGAGCATTATCAAACATTTGGGGATCCAAATCAATGGCACCTGCTGCCTGGAGGGAAAGATCTACAAACTGCTGGAG
CCCCTGGGATTCCAATACACCTTCATTAACAATTTT

Alignment

ORF - retro_sscr_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 72.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  NRGQIKDGKITKVFSAEDIRNLSPMVLRVQGP-SCILKKHRLLLHTSKEESDKARVYRPQKDSSSTFELV
          NR..I.....TKVFS...I.NLS...L.VQGP.SCILKK..L.LH...EES.K.RV..PQKD.SSTF.LV
Retrocopy NRIPINMSQLTKVFSTGEIKNLSQITLKVQGP<SCILKKPWLILHIPREESEKVRVCQPQKDNSSTFKLV

Parental  LGPGQHAYAL-GPLESDLKETFYVEALQFPSGSFPGLISYSVSLVEESKDGIGPQILVYKDTVVFRVAPC
          LGPG.H...L..PL...L.E.FY..AL.F.S..F.GLIS.SVSLVEES.D...P.IL.YKD.VVF.V.PC
Retrocopy LGPG*HTLPL<APLKDNLQENFYAKALEFLSTRFLGLIS*SVSLVEESQDLSIPEILAYKDLVVFWVTPC

Parental  IFTPSTQMPLEM-YVCRELQVQGFVNAVTELSERSNSQVASVYEDPNRLGRWLQDEMAFCYTQAP-HKTT
          IF.PST.MPLE...VCRELQVQG.VN.V.ELSERSNS.V....ED.N..GRW.QD.M.FC.TQAP.HKT.
Retrocopy IFSPST*MPLEV<IVCRELQVQGSVNTVMELSERSNS*VGIHLEDLNHSGRWQQDNMVFCFTQAP<HKTI

Parental  ALVLDTPRVTKLED-FPMRYSLSPG-IGYVTLNTLDHTVASIDSIGNLMVSPPVKVKGKEYPLGRILIGS
          .LVLDT....K....FP....LSPG..GY.T..T..H..ASIDSIGNLMVSP..K.KGKEYPLGRIL...
Retrocopy SLVLDTFYIPKINN<FPHEI-LSPG<VGYMTQHTQNHREASIDSIGNLMVSPLIKDKGKEYPLGRILTDN

Parental  SFYPSKDGR-DMSKALRDFLYAQQVQAPVELFSDWLMIGHIYEFMCFIPTQFKVEGKKDFRLLLASP-ST
          SFYPSK.G..DMSK...DFLYAQQ.Q.P.ELF.DWLMIGH..E.MC.IPT..KVEGKKDF.LLL.SP.S.
Retrocopy SFYPSKNGG>DMSKTPGDFLYAQQIQDPLELFLDWLMIGHTHELMCLIPT*YKVEGKKDFWLLLVSP<SS

Parental  CYKLFTEKQK-QGYGDA-ALFGEIRKEQLLSNGREALTINQLLADENMKKQNDYVERCIDLNRAILKREL
          CY..F.EKQ...GYGD...LFG.IRKEQLLSN.REA.TINQLL.DEN..K.NDYVE..I..NRAILKREL
Retrocopy CYRFFKEKQR<EGYGDV<TLFGKIRKEQLLSNRREANTINQLLTDENLRKHNDYVEKRINMNRAILKREL

Parental  GLAEKDIIDIPQLFCLEQIVNVP-SNELTGKLYARPYFPNLLQIIVMGQNLGIPKPFGPQINGACCLEEK
          .L.EK.I...PQLFCLEQI.N.P.SNE.T.KL.A......LLQIIVMGQNL.I.K..G.QING.CCLE.K
Retrocopy SLVEKEIMNNPQLFCLEQIDNAP<SNEQTRKLFANS-VSDLLQIIVMGQNLSIIKHLGIQINGTCCLEGK

Parental  IYELLEPLGFQCTFINDF
          IY.LLEPLGFQ.TFIN.F
Retrocopy IYKLLEPLGFQYTFINNF

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	0.14 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	0.31 RPM
SRP018856_adipose	0.00 RPM	0.05 RPM
SRP035408_brain	0.00 RPM	0.13 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_1118 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007733	2 retrocopies	retro_cjac_1086, retro_cjac_1210,
Sus scrofa	ENSSSCG00000003484	1 retrocopy	retro_sscr_1118 ,