RetrogeneDB ID: retro_sscr_953

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:112747798..112748482(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSK
• Ensembl ID: ENSSSCG00000001900
• Aliases: None
• Description: c-src tyrosine kinase [Source:HGNC Symbol;Acc:2444]

Sequence

>retro_sscr_953
GTCATGCAGCAATATATCTCAGATGAAGATGGACTCTGCATTTGCCTCACTAAGCCAAAGGTAATGGAGTAACAAACTGC
CAGCTCAGGATGAGTTTTTTGGCAGCTGGTGGATACTAAACACAAAGAAACTGAATCTTCTGCAGACTCTTGGGAAGCGG
GGGGTTAGAGAGTTGATGCTGGGCGATTACCCCAGAAAGAATGTCACTGTCAAGTTCATTAATGTGATACCACTTTGCAT
ACCTTCCTGGCTGAAGTCTCTGTCATAACACAACTTAGGCATAGCAACCAGATACAGCTTCTGGATATGATCGTGGAGAG
AAAGGTGGGCTCTACATATTACTGAGTGAATGGCTGTGGGGAGTCTGTGCTGTTGGATTGTCAACAGTGGCAGAGTTTGT
ATTGGGTGGGGATCATCTCCTCACACGTTCACTAGACACATTAGGGGCCATGGAATACATGCGGGGCAAAAACATTTTGC
GCAGAGACCTGGATGCCCTCACCATGGCTGGTGTTTGAGGACAGTGTAGCCAAAATCAGTGACTTGAGCCTCATCAAGAA
GATTTCCAGCACACAGGACTCAGGCAAGCTGCTGGTCAAGTAGACAACTCCCAAGACCCTGAGAGAGAGAAAAAATTCTC
CACAAGGTTTGATGTATGAAGTTCTCTGGAAAATCTCCTCCTTT

Alignment

ORF - retro_sscr_953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.27 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LVEHYTSDADGLCTRLIKPKLMEGTVA-AQDEFFRSGWALNMKDLKLLQTIGKGEFGDVMLGDYRGNKVA
          ....Y.SD.DGLC..L.KPK.ME...A.AQDEFF.S.W.LN.K.L.LLQT.GK......MLGDY....V.
Retrocopy VMQQYISDEDGLCICLTKPKVME*QTA>AQDEFFGSWWILNTKKLNLLQTLGKRGVRELMLGDYPRKNVT

Parental  VKCIK-NDATAQAFLAEASVMTQLRHSNLVQLLGVIVE-EKGGLYI-VTEYMAKGSLVDYLRSRGR-SVL
          VK.I...D.T...FLAE.SV.TQLRHSN..QLL..IVE.EKGGLYI..TE.MA.GSL.......GR..VL
Retrocopy VKFIN<CDTTLHTFLAEVSVITQLRHSNQIQLLDMIVE<EKGGLYI<ITE*MAVGSLCCWIVNSGR>FVL

Parental  GGDCLLKFSLDVCEAMEYLEGNNFVHRDLAARNV-LVSEDNVAKVSDFGLTKEASSTQDTGKLPVKWTAP
          GGD.LL..SLD...AMEY..G.N...RDL.A....LV.ED.VAK.SD..L.K..SSTQD.GKL.VK.T.P
Retrocopy GGDHLLTRSLDTLGAMEYMRGKNILRRDLDALTM>LVFEDSVAKISDLSLIKKISSTQDSGKLLVK*TTP

Parental  EALREKKFSTKSDVWSFGILLWEIYSF
          ..LRE.K.S...........LW.I.SF
Retrocopy KTLRERKNSPQGLMYE---VLWKISSF

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	57.07 RPM
SRP014902_testis	0.00 RPM	58.84 RPM
SRP018288_heart	0.00 RPM	11.39 RPM
SRP018288_kidney	0.00 RPM	20.59 RPM
SRP018288_liver	0.00 RPM	22.55 RPM
SRP018288_lung	0.00 RPM	96.94 RPM
SRP018856_adipose	0.00 RPM	43.70 RPM
SRP035408_brain	0.00 RPM	29.76 RPM
SRP035408_liver	0.00 RPM	20.55 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_953 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_953 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013581	1 retrocopy	retro_ecab_639,
Myotis lucifugus	ENSMLUG00000013625	1 retrocopy	retro_mluc_1162,
Sus scrofa	ENSSSCG00000001900	1 retrocopy	retro_sscr_953 ,