RetrogeneDB ID: retro_sscr_503

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:89354885..89355155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSSSCG00000009145
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_sscr_503
GCTCCAGTGGTGGTGTCTTCCTTCTCATCAAGGGAGGAGTGATTGGTGACATCAGGGTGGAACCTCCCAGTGTCGGTTCC
CTGACTCATGAACGTGGGCCTCTGAGGCCAGTTGCTTTCTTGGCCCACAGAGCAGATGGACAGTATGCTAGGAAGGACTT
GCCACCAGCTTCCTGTTTACAATGGAGGTTTAGGTTTCATAATCCTGGGCCGACCCAATGCCGCAAACATTCCGAAACTC
AATAGATTTCTTGTTCTCTTCATTGGATTT

Alignment

ORF - retro_sscr_503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.4 %
• Parental protein coverage: 61.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ALVVVSYF-LITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVNGQYIM-EGLASSFLFTM-GGLGF
          A.VVVS.F.LI.GG.I.D..VEPPSVGS.T.E.G..RPVAFLA.R..GQY...EGLA.SFLFTM.GGLGF
Retrocopy APVVVSSF<LIKGGVIGDIRVEPPSVGSLTHERGPLRPVAFLAHRADGQYAR<EGLATSFLFTM<GGLGF

Parental  IILDRSNAPNIPKLNRFLLLFIGF
          IIL.R.NA.NIPKLNRFL.LFIGF
Retrocopy IILGRPNAANIPKLNRFLVLFIGF

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	11.55 RPM
SRP014902_testis	0.00 RPM	34.65 RPM
SRP018288_heart	0.00 RPM	11.18 RPM
SRP018288_kidney	0.00 RPM	36.84 RPM
SRP018288_liver	0.00 RPM	103.14 RPM
SRP018288_lung	0.00 RPM	13.03 RPM
SRP018856_adipose	0.00 RPM	9.78 RPM
SRP035408_brain	0.00 RPM	15.34 RPM
SRP035408_liver	0.00 RPM	115.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_503 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_503 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110, retro_amel_165,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462, retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503 ,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,