RetrogeneDB ID: retro_sscr_510

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:117335875..117336163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOP16
• Ensembl ID: ENSSSCG00000029577
• Aliases: None
• Description: NOP16 nucleolar protein [Source:HGNC Symbol;Acc:26934]

Sequence

>retro_sscr_510
ATCCAGTGCTCCCACATCCATTACGCCTGGGACCAAACCAAATCGGTGCGGCAGAACCTGGCCGAGATGGGTTTGACTAT
GGACCCCAACAGGGCAGTGCCCCTTATTAAGAGAAAGGTAAAAGCCATGGAGGTGGACGGAGAGGAGAGGCTGAAGGAGC
TTGTGTGGAAGCCCTATGTGCTCAATGACCTAGAGGGAGAAGCCAGCCTTCCAGAAAAGAAAGGAAATATGCTGTCTCGG
GACCTCATTAACTGCGTTTGCTATATGGTGGAGAACCATGGAGAGGAC

Alignment

ORF - retro_sscr_510 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.54 %
• Parental protein coverage: 73.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IQCSHIRHAWDQTKSVRQNLAEMGLAMDPNRAVPLIKRKVKAMEVDREERPKELVRKPYVLNDLEAEASL
          IQCSHI..AWDQTKSVRQNLAEMGL.MDPNRAVPLIKRKVKAMEVD.EER.KELV.KPYVLNDLE.EASL
Retrocopy IQCSHIHYAWDQTKSVRQNLAEMGLTMDPNRAVPLIKRKVKAMEVDGEERLKELVWKPYVLNDLEGEASL

Parental  PEKKGNTLSRDLIDYVRYMVENHGED
          PEKKGN.LSRDLI..V.YMVENHGED
Retrocopy PEKKGNMLSRDLINCVCYMVENHGED

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	11.15 RPM
SRP014902_testis	0.00 RPM	14.85 RPM
SRP018288_heart	0.05 RPM	12.28 RPM
SRP018288_kidney	0.00 RPM	32.11 RPM
SRP018288_liver	0.16 RPM	20.79 RPM
SRP018288_lung	0.10 RPM	18.23 RPM
SRP018856_adipose	0.00 RPM	34.18 RPM
SRP035408_brain	0.06 RPM	40.18 RPM
SRP035408_liver	0.06 RPM	40.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_510 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016694	2 retrocopies	retro_cfam_1790, retro_cfam_1793,
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208,
Cavia porcellus	ENSCPOG00000026072	1 retrocopy	retro_cpor_129,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Myotis lucifugus	ENSMLUG00000003504	1 retrocopy	retro_mluc_2425,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Mus musculus	ENSMUSG00000025869	2 retrocopies	retro_mmus_3033, retro_mmus_3258,
Otolemur garnettii	ENSOGAG00000000824	2 retrocopies	retro_ogar_1323, retro_ogar_2299,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510 ,
Ictidomys tridecemlineatus	ENSSTOG00000004869	1 retrocopy	retro_itri_1124,