RetrogeneDB ID: retro_sscr_661

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:17379913..17380642(-)
• Located in intron of: ENSSSCG00000013262

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTPBP10
• Ensembl ID: ENSSSCG00000015305
• Aliases: None
• Description: GTP-binding protein 10 (putative) [Source:HGNC Symbol;Acc:25106]

Sequence

>retro_sscr_661
CCTCAGAAACAGTTTGTGGCTGGAGAAGGAGTGAACAGTCGAGTTAGTGCACTGAATGGCTCAAAAGGAAAAGACTGTGA
AATTCCTGTACCTGTGGGTATTTCAATAACTGATGAAAATGGTAAAATTATAGGAGAATTCAATAAAGAGAAAGACAGAA
TTCTAGTAGCTGAAGAAAGTCTTGGTGGTAAATTACTTACAAATTTCTTACCATTGAAAGGCCAGAAACAAGTAATTCAC
CTTGATCTAAAACTTATAGCTGATATATACCTAGTGTGATTCCCAAATGCTGGAAAATCCTCTTTGCTAAGTAAAATTTC
TCATGCAAAACCTGTGAATGCAGATTATGCATTTTCAACATGAAAACCTGAACTTCAAAAAATTAAGTATCATGGTTTCA
AAGAGATACCAATAGCTGATCTTCCTGGTTTAATAGAAGGAACACATATGAACAAAGGAATGGGCCACAAAGTCCTCAGG
CATATAGAAAGAACTAAATAATTACTTTTTGTTGTTGGTATTTCTGGATTTCAGCTTTCTTTCCAAACTCAATATAGAAC
TGCCTTCGAAACTGTAATACTACTCACAAAAGAGTTGGAGTTGCCCAAAGAGGAACTTCAGACAAAACCTGATGTCCTAG
CAGTTAATAAAATGGACTTGACAGATGCCCAAGATAAATTTCAAGTACTGATGAACTAACTCCAAAATCCTAAAGACTGT
TTACATTTA

Alignment

ORF - retro_sscr_661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.61 %
• Parental protein coverage: 62.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQKRFVAGEGANSRVSALKGSKGKDCEIPVPVGISVTDENGKIIGELNKEKDRILVAEGGIGGKLLTNFL
          PQK.FVAGEG.NSRVSAL.GSKGKDCEIPVPVGIS.TDENGKIIGE.NKEKDRILVAE...GGKLLTNFL
Retrocopy PQKQFVAGEGVNSRVSALNGSKGKDCEIPVPVGISITDENGKIIGEFNKEKDRILVAEESLGGKLLTNFL

Parental  PLKGQRRVIHLDLKLIADVGLVGFPNAGKSSLLSKISHAKPAIADYAFTTLKPELGKIMYNDFKQISVAD
          PLKGQ..VIHLDLKLIAD..LV.FPNAGKSSLLSKISHAKP..ADYAF.T.KPEL.KI.Y..FK.I..AD
Retrocopy PLKGQKQVIHLDLKLIADIYLV*FPNAGKSSLLSKISHAKPVNADYAFST*KPELQKIKYHGFKEIPIAD

Parental  LPGLIEGAHMNKGMGHKFLKHIERTKQLLFVVDISGFQLSSQTRYRTAFETIILLTKKELELYKEELQTK
          LPGLIEG.HMNKGMGHK.L.HIERTK.LLFVV.ISGFQLS.QT.YRTAFET.ILLT.KELEL.KEELQTK
Retrocopy LPGLIEGTHMNKGMGHKVLRHIERTK*LLFVVGISGFQLSFQTQYRTAFETVILLT-KELELPKEELQTK

Parental  PALLAVNKMDLPDAQDKFQVLMNQLQSPKDFLHL
          P..LAVNKMDL.DAQDKFQVLMN.LQ.PKD.LHL
Retrocopy PDVLAVNKMDLTDAQDKFQVLMN*LQNPKDCLHL

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	1.19 RPM
SRP014902_testis	0.00 RPM	9.48 RPM
SRP018288_heart	0.03 RPM	17.26 RPM
SRP018288_kidney	0.00 RPM	18.62 RPM
SRP018288_liver	0.00 RPM	9.59 RPM
SRP018288_lung	0.00 RPM	12.83 RPM
SRP018856_adipose	0.00 RPM	12.63 RPM
SRP035408_brain	0.00 RPM	20.68 RPM
SRP035408_liver	0.00 RPM	14.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_661 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_661 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_661 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014212	1 retrocopy	retro_cjac_563,
Myotis lucifugus	ENSMLUG00000007418	1 retrocopy	retro_mluc_789,
Mus musculus	ENSMUSG00000040464	1 retrocopy	retro_mmus_3183,
Oryctolagus cuniculus	ENSOCUG00000014847	1 retrocopy	retro_ocun_1558,
Otolemur garnettii	ENSOGAG00000010568	1 retrocopy	retro_ogar_431,
Sus scrofa	ENSSSCG00000015305	1 retrocopy	retro_sscr_661 ,