RetrogeneDB ID: retro_sscr_634

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:113985655..113986012(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSSSCG00000029741
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_sscr_634
ATTGCTGTATTTATTCCTGAATCGCCTGGGCTGGAGGACTATGCTGCAGTTAAAGACAACTACTTCCAGAATGGGGAGGG
TTTCCGCTGTCTCCACTATTACAGAAATTGAATCCTTTGCAGCCACAGCTGGTTTCAGGAGCATATGTTAAGAATAAAAG
AAGATAAGAATGTTTAATTTTCTCCAGTTGGTTACAAATCAGATTTAGGAGATAAAAGCAAGGTTTATGTAGAAGAGGCA
AAAACCAGAGCCAATCAGTGGAATGTTAACTATGTGGAAACATCTGCTAAAATGTGAACTAATGTTAACAAGGTAATGTT
TGATTTAATGAGGGAATTTCAAGTCAGAAAGATGGAA

Alignment

ORF - retro_sscr_634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 58.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQIDILDTAGQEDYAAIRDNYFRSGE-GF-LCVFSITELESFAATADFR-EQILRVKEDENVPFLLVGNK
          ....I....G.EDYAA..DNYF..GE.GF...V..ITE.ESFAATA.FR.E..LR.KED.NV.F..VG.K
Retrocopy IAVFIPESPGLEDYAAVKDNYFQNGE<GF<SAVSTITEIESFAATAGFR<EHMLRIKEDKNV*FSPVGYK

Parental  SDLEDKRQVSVEEAKTRADQWNVNYVETSAKTRANVDKVFFDLMREIRARKME
          SDL.DK..V.VEEAKTRA.QWNVNYVETSAK...NV.KV.FDLMRE...RKME
Retrocopy SDLGDKSKVYVEEAKTRANQWNVNYVETSAKM*TNVNKVMFDLMREFQVRKME

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	83.62 RPM
SRP014902_testis	0.00 RPM	73.98 RPM
SRP018288_heart	0.00 RPM	33.87 RPM
SRP018288_kidney	0.00 RPM	42.65 RPM
SRP018288_liver	0.00 RPM	22.39 RPM
SRP018288_lung	0.00 RPM	48.98 RPM
SRP018856_adipose	0.00 RPM	44.59 RPM
SRP035408_brain	0.00 RPM	143.91 RPM
SRP035408_liver	0.00 RPM	63.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_634 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_634 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_634 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634 ,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,