RetrogeneDB ID: retro_sscr_132

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:198377669..198377873(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSSSCG00000013597
• Aliases: None
• Description: Sus scrofa ribosomal protein S28 (RPS28), mRNA. [Source:RefSeq mRNA;Acc:NM_001001587]

Sequence

>retro_sscr_132
ATGGACACAAGCAGTGTGCCACCCATCAAGATTGCCTGGGACACCAAGGTGCTAGACAGGACTGATTTGCAAAGACAGTG
CACACAGGTGTTTGTAGAATTCATAGATGACAACAGCTGCTCCATCATCTGAAATGTGAGAGTCCCCATACATGACAGTG
ACATGCTCACCTTTGTGGAGTCAGAATAAGAGGCTCAGAGGCTG

Alignment

ORF - retro_sscr_132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.24 %
• Parental protein coverage: 98.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL
          MDTS.V.PIK.A..TKVL.RT..Q.QCTQV.VEF.DD.S.SII.NV..P....D.LT..ESE.EA.RL
Retrocopy MDTSSVPPIKIAWDTKVLDRTDLQRQCTQVFVEFIDDNSCSII*NVRVPIHDSDMLTFVESE*EAQRL

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	706.39 RPM
SRP014902_testis	0.00 RPM	1306.26 RPM
SRP018288_heart	0.00 RPM	245.80 RPM
SRP018288_kidney	0.00 RPM	368.02 RPM
SRP018288_liver	0.00 RPM	300.95 RPM
SRP018288_lung	0.00 RPM	61.40 RPM
SRP018856_adipose	0.00 RPM	1019.51 RPM
SRP035408_brain	0.00 RPM	179.83 RPM
SRP035408_liver	0.00 RPM	109.76 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_132 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_132 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Felis catus	ENSFCAG00000024931	3 retrocopies	retro_fcat_1130, retro_fcat_611, retro_fcat_752,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Oryctolagus cuniculus	ENSOCUG00000021484	2 retrocopies	retro_ocun_1230, retro_ocun_1799,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,
Sus scrofa	ENSSSCG00000013597	3 retrocopies	retro_sscr_132 , retro_sscr_191, retro_sscr_808,