RetrogeneDB ID: retro_sscr_234

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:78525724..78527581(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDZD8
• Ensembl ID: ENSSSCG00000010669
• Aliases: None
• Description: PDZ domain containing 8 [Source:HGNC Symbol;Acc:26974]

Sequence

>retro_sscr_234
ATGGGGCTGCTGCTCATAATCCTGGTATTAGTGTGCTTGTCTCCTTTCTCAAGCTCCTCACCTAGTTCCTGCTTCTTTAC
CACAAACAACCCAAGCCACTGCCTGAGGAGGCTACCAGTGTGGCTGAGGGCTTATGCTACATCAAGCAGGTGCTGGGATG
TATGTGGGAGTATGTTTATGGTGGCAGGGGTACTTAGGAGAACCTCCAGCTGCCTGTGATCATGGTGTGACCCTGAGCCC
TGAGACCCTTGCACCACAGACATCAGAGAACTGCTTCTTCCTCAATGTCACCATCCTGTTCCTGTTCCCAGAGCTGTGGG
ACACAGTGCTGGACAACTGCTGGGTCACCAAGAAAATCCAGGTGGAGTTTGAGGAGCTGCTGCAGACCAAGCACATGGTT
GACTGCCGGAGGGGCTGAGCCTGAGGAATGTGTTCCTGGGCAAGACTATGCCCTTCAACAAGACCATCTGTCTTCTCCAG
CCAGTGGTGGAGAAGCCACCTGGGAGCCTGATGGCCCTGAGGGGGAGAACTGGCTGACACATCCCCTGAGGAGCTGGCCT
TGCAGTCAGAGGTGGAGTACAATGTGGGCTTCCACTTGGCCATCAATGTAGACCTGGTCTTTGGCAAGTCCACCTACCTC
TTCCTCAAGCTGTCTGGGGTGATGAGGAGGCTGTGTTTTTTCCTCACCAGAATGTCCATCACCCACTGGTTCTTCTCTTT
TGTGGAGGACCCACTGATCAAATTTGAGGTGTGCTCCCAGTTTGAAAGGTGGCCCATTCCCCAGCTCACCTCCATCATCA
TCTACCAGCACAAGAAAATCATCAAGTGCAAGTACACCCTCCCAAGCTACAAGATTAATTTTAAGCCATTTTTCCCATTC
CAAGCCTTGCAAGGATTTTAAGAAAATGAAGAAGGCATAACCATATACAACAAGGGACACTTACTTAGGGCTGCCTTAAA
ATTACAGTGTTAGAATATAGCAGATTACATATTTTTGGATCCTATGATAGAGAGGCAAATATTCATTGCACACCTGAGCT
GAGCAGTGGGGTTTGGGAAGAAAAACAAAGGAGTTCTATTAAGATGGTTGAATTAATAAAGGGAAATTTCCAAAGTTTTG
GACTTACACTTCCTCTGGTCCCGTCAACTGACAGGTATGCTGGGTACCTCATAATTTACATGGAGGCCCCAAACTCACCT
GCTGAAATTGCAGATCTTCAGAGAGGAGACTGACTGATTTCTATTGAAAGTATGAAAATCACATATACACTGCAAGTATT
GAAGTTTATCAAGCAGGCTGGCAACCAATTCCTGGTGTATTACAAAAGTCCTGTTGGCCAGAGCAATCAGAGTATGCTGC
AGCAAGATAATTTTGGACAGTTGGAAGAAAACACTGTGAAGCTCATGTCAGGCAAACTATGAAGAAGAAACAACTGGGTT
GGCAATAGATGCTGAAAATAGAAACCTGGATTCTGAAATTGAAGGCTTGAGTGTGATGTCAGAGCACAAACTGAGGTCAA
AGATGAGGCATAGTCATGAAGTCACCATCCCAAACATATTCTGACAACACTTTTTATTAAACGTCTTGGAACTATTTCAC
CAGTTTTAAACCAAAAATTAGCTGTATGAGGTCACTCACCACCAGCAAAACGTCCATCCAAAGAAGGACATAAATCCTTA
GCCCTGAAATCTTCTGAGATAACAGACCCAGCACAAATGCCAAAATCCTCCCAAGGATCCAATTTCAAACCACCTGTGCC
ACCATGACTGCAAGTAAAAATTCCTTTGCCTTATTCTGAAGCCATAAATCAGGAAGAATCAGATATTCCTGTTGAAAAAC
CAGAGAAGGTGCTACTG

Alignment

ORF - retro_sscr_234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.89 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MGLLLMILAS-AVLGSFLTLLTQFLLLYRKQPLPPPDEAARAAEGFRYIKPV-PGLALREYLYGGGGAEE
          MGLLL.IL....VL.SFL.LLT.FLLLY.KQP.P.P.EA...AEG..YIK.V..G......L...G...E
Retrocopy MGLLLIILVL<SVLVSFLKLLT*FLLLYHKQPKPLPEEATSVAEGLCYIKQV<AGMYVGVCLWWQGYLGE

Parental  PAGGSPEGGATPTPETPAPPTRETCYFLNATILFLFRELRDTALARRWVTKKIKVEFEELLQTK-TAGRL
          P.......G.T..PET.AP.T.E.C.FLN.TILFLF.EL.DT.L...WVTKKI.VEFEELLQTK...G.L
Retrocopy PPAAC-DHGVTLSPETLAPQTSENCFFLNVTILFLFPELWDTVLDNCWVTKKIQVEFEELLQTK<AHG*L

Parental  LEGLSLRDVFLGETVPFIKTIRLLRPVVPS-ATGEPDGPEGE-ALPATSPEELAFEAEVEYDGGFHLAID
          .EGLSLR.VFLG.T.PF.KTI.LL.PVV...AT.EPDGPEGE..L..TSPEELA...EVEY..GFHLAI.
Retrocopy PEGLSLRNVFLGKTMPFNKTICLLQPVVEK<ATWEPDGPEGE<ELADTSPEELALQSEVEYNVGFHLAIN

Parental  VDLVFGKSAYLFVKLSRVEGRLRFVLTRVPFTHWFFSFVEDPLIDFEVRSQFEGRPMPQLTSIIVNQLKK
          VDLVFGKS.YLF.KLS.V..RL.F.LTR...THWFFSFVEDPLI.FEV.SQFE..P.PQLTSII..Q.KK
Retrocopy VDLVFGKSTYLFLKLSGVMRRLCFFLTRMSITHWFFSFVEDPLIKFEVCSQFERWPIPQLTSIIIYQHKK

Parental  IIKRKHTLPSYKIRFKPFFPFQTLKGFEEEEE-EHIHIQQWALTEGRLKVTLLECSRLLIFGSYDREANI
          IIK.K.TLPSYKI.FKPFFPFQ.L.GF.E.EE..H.HIQQ..LT.G.LK.T.LE.SRL.IFGSYDREANI
Retrocopy IIKCKYTLPSYKINFKPFFPFQALQGF*ENEE<RHNHIQQGTLT*GCLKITVLEYSRLHIFGSYDREANI

Parental  HCTLELSSGVWEEKQRSSIKTVELIKGNLQSVGLTLRLVQSTDGYAGHVIIETVAPNSPAAVADLQRGDR
          HCT.ELSSGVWEEKQRSSIK.VELIKGN.QS.GLTL.LV.STD.YAG..II...APNSPA..ADLQRGD.
Retrocopy HCTPELSSGVWEEKQRSSIKMVELIKGNFQSFGLTLPLVPSTDRYAGYLIIYMEAPNSPAEIADLQRGD*

Parental  LIAIGGVKITSTLQVLKLIKQAGDRVLVYYERPVGQSNQSVVLQDNFGQLEENFL-SSSCQPTYEEETTG
          LI.I...KIT.TLQVLK.IKQAG...LVYY..PVGQSNQS...QDNFGQLEEN...SS......EE.T.G
Retrocopy LISIESMKITYTLQVLKFIKQAGNQFLVYYKSPVGQSNQSMLQQDNFGQLEENTV>SSCQANYEEETT-G

Parental  LAIDAENRDLDSEFEDLA-SDVRAQTEVKDEAQSLSHSPKRIPTTLSVKPLGTISPVLNRKLAVGGHPPP
          LAIDAENR.LDSE.E.L...DVRAQTEVKDEA.S.SH.PK.I.TTL..K.LGTISPVLN.KLAV.GH.PP
Retrocopy LAIDAENRNLDSEIEGLS<CDVRAQTEVKDEA*S*SHHPKHILTTLFIKRLGTISPVLNQKLAV*GHSPP

Parental  PKLPSKEGHKSLALKSSEITEPAQMSKPTQGSTFKPPVPPRPQVKIPLPSADTPNQAELDIPVEKPEKVT
          .K.PSKEGHKSLALKSSEIT.PAQM.K..QGS.FKPPVPP..QVKIPLP.....NQ.E.DIPVEKPEKV.
Retrocopy AKRPSKEGHKSLALKSSEITDPAQMPKSSQGSNFKPPVPP*LQVKIPLPYSEAINQEESDIPVEKPEKVL

Parental  L
          L
Retrocopy L

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	19.25 RPM
SRP014902_testis	0.00 RPM	29.56 RPM
SRP018288_heart	0.00 RPM	40.52 RPM
SRP018288_kidney	0.00 RPM	18.22 RPM
SRP018288_liver	0.00 RPM	8.00 RPM
SRP018288_lung	0.00 RPM	46.94 RPM
SRP018856_adipose	0.00 RPM	34.14 RPM
SRP035408_brain	0.00 RPM	13.28 RPM
SRP035408_liver	0.00 RPM	4.49 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_234 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_234 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_234 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000002691	1 retrocopy	retro_pabe_1449,
Sus scrofa	ENSSSCG00000010669	1 retrocopy	retro_sscr_234 ,