RetrogeneDB ID: retro_sscr_924

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:2475493..2475682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSSSCG00000003858
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:HGNC Symbol;Acc:25930]

Sequence

>retro_sscr_924
CCTCGAGATGACATCCTCAGTAGGCGGGAAAGGTCAAAAGATGCCAGCCCCATCAGTAGGTGGTCTCCTGCCCGAAGAAG
AGCCAGTCGGTCTCCGGTCAGAAGGAGGTCCCGATCCCCCCTCAGACGCAGCCGGTCTCCCAGAAGAAGAAGCCGATCTC
CTCGGAGGAGGTAACGACGCCCGTTTGAT

Alignment

ORF - retro_sscr_924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.52 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSPDHRRRSYRDLDKPRRSPTLRYRRSRSRSP-RRRSRSPKRRSPSPRRERHRSKSPRRHRSRSRD
          P..D...R..R..D....S.....RR..SRSP.RRRSRSP.RRS.SPRR...RS.SPRR...R..D
Retrocopy PRDDILSRRERSKDASPISRWSPARRRASRSPVRRRSRSPLRRSRSPRR---RSRSPRRR*RRPFD

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	1.59 RPM	5.57 RPM
SRP014902_testis	4.67 RPM	6.93 RPM
SRP018288_heart	2.04 RPM	4.85 RPM
SRP018288_kidney	4.93 RPM	6.99 RPM
SRP018288_liver	2.24 RPM	4.32 RPM
SRP018288_lung	9.16 RPM	8.35 RPM
SRP018856_adipose	0.81 RPM	8.87 RPM
SRP035408_brain	1.91 RPM	16.45 RPM
SRP035408_liver	3.29 RPM	12.18 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_924 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_924 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924 ,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,