RetrogeneDB ID: retro_sscr_859

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:21980889..21981743(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHEK1
• Ensembl ID: ENSSSCG00000015215
• Aliases: None
• Description: checkpoint kinase 1 [Source:HGNC Symbol;Acc:1925]

Sequence

>retro_sscr_859
GAGCCAGACATAGGCATGCCTGAACAAGATGCTCAGAGGTTCTTCCATCAACTCATGGCAGGGGTGGTTTATCTGCATGG
TATTGGAATAACTCACAGGGATATTAAGCCAGAAAGTCTCCTAATGGATGAAAGGGATAACCTCAAAATCTCTGACTTCA
GCTTGGCAACCGTTTTTCGGCACAATAATCGTGAGCGTTTATTGAACAAGATGTGTGGTACTTTACCATATGTTGCTCTG
AAGAGAAAAGAATTTCATGCAGAACCAGTTGATGTTTGGTCTTGTGGAATAGTACTTACTGCAATGTTGGCTGGAGAACT
GCCATGGGACTAGCCTCGTGACAGTTGTCAGGAATATTGCGATTGGAAAGAAAAAAAAACATACCTCAACCCTTGGAAAA
AAATCGATTCTGCTCCTCTAGCCCTGCTGCATAAAATCCTAGTTGAGAATCCATCAGTAAGGATTACCATCCCAGACATC
AAAAAAGATAGATGGATAGATGGTACAACAAACCACTTAAGAAAGGGGCAAAGAGGCCCCGAGTCACTTCAGGTGGTGTA
TCAGAGTCTCCTAGTGGATTCTCTAAGCATTTTCAATCCAATTTGGACTTTTCTCCAGTAAATAGTGCTTCTAGTGAAGA
AAATGTGAAGTACTCCAGTTCTCAGCCAGAACCACGGACAGGTCTTTCCTTACGGGACACCAGCCCTTCCTACATTGATA
AACTGGTACAAGGGATCAGTTTTTCCCAGCCCACATGCCCTGATCATATGCTCCTGAATAGTCAGTTACTTGGCACCCCA
GGATCCTCACAGAACCCCTGGCAGCACCTGGTCAAAAGAATGACACGATTATTT

Alignment

ORF - retro_sscr_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 60.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPDIGMPEQDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERGLDNLKISDFGLATVFRHNNRERLL
          EPDIGMPEQDAQRFFHQLMAGVVYLHGIGITHRDIKPE.LL.DER..DNLKISDF.LATVFRHNNRERLL
Retrocopy EPDIGMPEQDAQRFFHQLMAGVVYLHGIGITHRDIKPESLLMDER--DNLKISDFSLATVFRHNNRERLL

Parental  NKMCGTLPYVAPELLKRKEFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYCDWKEKKTYLNPWKKI
          NKMCGTLPYVA...LKRKEFHAEPVDVWSCGIVLTAMLAGELPWD.P.DSCQEYCDWK....YLNPWKKI
Retrocopy NKMCGTLPYVA---LKRKEFHAEPVDVWSCGIVLTAMLAGELPWD*PRDSCQEYCDWKXXXXYLNPWKKI

Parental  DSAPLALLHKILVENPSVRITIPDIKKDRWYN---KPLKKG-AKRPRVTSGGVSESPSGFSKHIQSNLDF
          DSAPLALLHKILVENPSVRITIPDIKKDRW.......L.KG.AKRPRVTSGGVSESPSGFSKH.QSNLDF
Retrocopy DSAPLALLHKILVENPSVRITIPDIKKDRWIDGTTNHLRKG<AKRPRVTSGGVSESPSGFSKHFQSNLDF

Parental  SPVNSASSEENVKYSSSQPEPRTGLSLWDTSPSYIDKLVQGISFSQPTCPDHMLLNSQLLGTPGSSQNPW
          SPVNSASSEENVKYSSSQPEPRTGLSL.DTSPSYIDKLVQGISFSQPTCPDHMLLNSQLLGTPGSSQNPW
Retrocopy SPVNSASSEENVKYSSSQPEPRTGLSLRDTSPSYIDKLVQGISFSQPTCPDHMLLNSQLLGTPGSSQNPW

Parental  QRLVKRMTRFF
          Q.LVKRMTR.F
Retrocopy QHLVKRMTRLF

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	0.80 RPM
SRP014902_testis	0.00 RPM	7.64 RPM
SRP018288_heart	0.00 RPM	1.47 RPM
SRP018288_kidney	0.00 RPM	2.36 RPM
SRP018288_liver	0.00 RPM	0.64 RPM
SRP018288_lung	0.00 RPM	3.26 RPM
SRP018856_adipose	0.00 RPM	1.04 RPM
SRP035408_brain	0.00 RPM	0.95 RPM
SRP035408_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_859 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_859 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
Cavia porcellus	ENSCPOG00000026175	1 retrocopy	retro_cpor_392,
Sus scrofa	ENSSSCG00000015215	1 retrocopy	retro_sscr_859 ,