RetrogeneDB ID: retro_sscr_365

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:26426076..26426389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAX1BP3
• Ensembl ID: ENSSSCG00000017866
• Aliases: None
• Description: Tax1 (human T-cell leukemia virus type I) binding protein 3 [Source:HGNC Symbol;Acc:30684]

Sequence

>retro_sscr_365
GAGTTGTGTCAAGGTGAGAACTTAATCCTGGGCTTCCGCATTGGAGGCAGAATTGACTAGGATCCCTCCCCAAATCCTTT
CTCAGATTAAGCAGGCAAAGGCATTTACAGTCACACACATATCTGAAGGAGGCCCTGTAGAAATGGCTGAGCTGCAGACT
GGGGACAAAATCATGCAGATGAACAGCTGGGCAATGACCATGATCACACGCAACCAGCGCTGGAAGCAGCTCATCAAGTA
CTCAGAGGAGGTGAGCCGTCTGCTGGTGATGAGACAGTCACTGCAGAAGGTGGTGCAGCAGTCCATGCTATCC

Alignment

ORF - retro_sscr_365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 84.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIY-VTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMV
          .L.QGENLILGF.IGG.ID.DPS.NPFS.D...KGIY.VT..SEGGP.E.A.LQ.GDKIMQ.N.W.MTM.
Retrocopy ELCQGENLILGFRIGGRID*DPSPNPFS-D*AGKGIY>VTHISEGGPVEMAELQTGDKIMQMNSWAMTMI

Parental  THDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSMLS
          T..Q..K.L.K.SEEV.RLLV.RQSLQK.VQQSMLS
Retrocopy TRNQRWKQLIKYSEEVSRLLVMRQSLQKVVQQSMLS

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	99.15 RPM
SRP014902_testis	0.00 RPM	42.72 RPM
SRP018288_heart	0.00 RPM	37.80 RPM
SRP018288_kidney	0.00 RPM	46.99 RPM
SRP018288_liver	0.00 RPM	8.16 RPM
SRP018288_lung	0.00 RPM	100.50 RPM
SRP018856_adipose	0.00 RPM	38.48 RPM
SRP035408_brain	0.00 RPM	4.48 RPM
SRP035408_liver	0.00 RPM	8.45 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_365 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_365 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000023829	1 retrocopy	retro_dnov_2238,
Dipodomys ordii	ENSDORG00000013801	2 retrocopies	retro_dord_56, retro_dord_728,
Myotis lucifugus	ENSMLUG00000026421	1 retrocopy	retro_mluc_221,
Mus musculus	ENSMUSG00000040158	1 retrocopy	retro_mmus_1929,
Oryctolagus cuniculus	ENSOCUG00000023903	1 retrocopy	retro_ocun_781,
Sus scrofa	ENSSSCG00000017866	1 retrocopy	retro_sscr_365 ,
Ictidomys tridecemlineatus	ENSSTOG00000022920	1 retrocopy	retro_itri_134,