RetrogeneDB ID: retro_sscr_360

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:200801251..200801702(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA1
• Ensembl ID: ENSSSCG00000004518
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 1 [Source:HGNC Symbol;Acc:28109]

Sequence

>retro_sscr_360
TGTGGTCAAGAAACCTACCTTGAAGACTACATTAAATAAAATAGGAGATGAGGTCATTGTAGTAAATGAATTTCTAAATA
AACTGGAATTGGAAATTGAGTATCAAGAACAAACCAACAGTTCACACAAGGAACTCTGTGAATCTCTTAAAGAAGATTAT
AAAGATGTGGAATATTTCAAAGAAAATATCCCTCCCCATTCTCCTCAAGTAACAGTAACCCAGAATGTTGTTAATGCATC
AGATCTTGGCCCTGAAGAACCAGCCAAGATTGAGGAATACGAACCCCCAAAAAAGCCCCCCAAAGAACAAAAAAAGTTAA
GGGAAATGTGATTTATAACTTCTGATGAGTTTAAAGGCATTACTGCATACATGAAATCTTGCTTAACCTATTGTCAAATT
AATGATGTTATTAAAGAAATCAACAAGGCGGTGGTTGGTAAATATAAAATA

Alignment

ORF - retro_sscr_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.81 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CGQE-PTLKTILNKIGDEIIVVNELLNKLELEIEYQEQTNSSLQELCESLEEDYKDVEHLKENIPPHLPQ
          CGQE.PTLKT.LNKIGDE.IVVNE.LNKLELEIEYQEQTNSS..ELCESL.EDYKDVE..KENIPPH.PQ
Retrocopy CGQE>PTLKTTLNKIGDEVIVVNEFLNKLELEIEYQEQTNSSHKELCESLKEDYKDVEYFKENIPPHSPQ

Parental  VTVTQNVVNGSDLDPEEPAKVEESAPPKKPPKEQRNIKEMLFITSDEFNGIPAYMKSRLTYCQINDVIKE
          VTVTQNVVN.SDL.PEEPAK.EE...............EM.FITSDEF.GI.AYMKS.LTYCQINDVIKE
Retrocopy VTVTQNVVNASDLGPEEPAKIEEYXXXXXXXXXXXXLREM*FITSDEFKGITAYMKSCLTYCQINDVIKE

Parental  INKAVVGKYKI
          INKAVVGKYKI
Retrocopy INKAVVGKYKI

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	0.13 RPM
SRP014902_testis	0.00 RPM	0.71 RPM
SRP018288_heart	0.00 RPM	0.42 RPM
SRP018288_kidney	0.00 RPM	0.59 RPM
SRP018288_liver	0.00 RPM	0.64 RPM
SRP018288_lung	0.00 RPM	2.75 RPM
SRP018856_adipose	0.00 RPM	0.08 RPM
SRP035408_brain	0.00 RPM	0.67 RPM
SRP035408_liver	0.00 RPM	4.23 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_360 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008555	2 retrocopies	retro_cjac_1103, retro_cjac_875,
Dasypus novemcinctus	ENSDNOG00000000190	1 retrocopy	retro_dnov_1081,
Loxodonta africana	ENSLAFG00000005238	1 retrocopy	retro_lafr_849,
Myotis lucifugus	ENSMLUG00000013388	1 retrocopy	retro_mluc_2127,
Sus scrofa	ENSSSCG00000004518	1 retrocopy	retro_sscr_360 ,
Tursiops truncatus	ENSTTRG00000015539	1 retrocopy	retro_ttru_1083,