RetrogeneDB ID: retro_sscr_499

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:81632065..81632325(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000000408
• Aliases: None
• Description: None

Sequence

>retro_sscr_499
TCCTGTGCTATTTACTTTCAGAAAGTGAATCATTTTGATCCCTTTACTATTCTAGCCATAAACTCCATCTGCCATGAATT
GGATACTATTCCCACTAGTGATGAGCGAAAAGAGGAGAAGGAAGTTGAATCTGGTATCAAACACAGAATCTATAAGACCA
GTCTAGCTATTTATGTAAAAGTTTCTGAACAGTTTCTTGAAAGTTTAAGTACATCCCAAAAGGAGAAGTAATCAGGAAGA
GTGATTTACAAAAGCGCTTC

Alignment

ORF - retro_sscr_499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.44 %
• Parental protein coverage: 52.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVPIDLQKVDQFDPFTVPTISSICHELDAISTNEEEK-ENGAESGIKHRTRDYKKTSLAPFVKVFEQFLE
          S..I..QKV..FDPFT...I.SICHELD.I.T..E.K.E...ESGIKHR.....KTSLA..VKV.EQFLE
Retrocopy SCAIYFQKVNHFDPFTILAINSICHELDTIPTSDERKEEKEVESGIKHR---IYKTSLAIYVKVSEQFLE

Parental  NLDRSR-KGELLKKSDLQKDF
          .L..S..KGE...KSDLQK.F
Retrocopy SLSTSQ<KGEVIRKSDLQKRF

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.14 RPM
SRP018288_heart	0.00 RPM	0.65 RPM
SRP018288_kidney	0.00 RPM	0.79 RPM
SRP018288_liver	0.00 RPM	1.12 RPM
SRP018288_lung	0.00 RPM	1.22 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	1.68 RPM
SRP035408_liver	0.00 RPM	1.32 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_499 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_499 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499 ,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,