RetrogeneDB ID: retro_sscr_247

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:37863070..37863526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL1
• Ensembl ID: ENSSSCG00000016044
• Aliases: None
• Description: ORM1-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:16036]

Sequence

>retro_sscr_247
AATGTTGGTATTTCCCACAGAGAGGTAAATCCAAATACCTGGGTAATGAATAGCCGAGGTATGTGGCTGACATATGCATT
GGGAGTTGGCTTGCTTCATATTGTTTTACTTAGTATTCCCTTCCTCAGTGTTCCTGTTGCTTGGACCTTAACAAATGTTA
TACATAAGCTGGGGATGTATGTATTTTTGCACACAGTAAAAGGAACACCTTTTGAAACTCCTGACCAGGGTAAAGCAAAG
CTCCTAACTCACTGGGAATAATCGGACTATGGAATACAGTTTACATCTTCATGGAAGTTTTTCACAATTTCTCCAATAAT
TCTATACTTCCTGGCAAGTTTCTATACGAAGTATGATCCAACTCACCTCATCCTTAACACAACTTCTCTCCTGAGTGTGC
TAATTCTCAAAATGCCACAGCTACATGGTGTTCAGATCTTTGGAATTAATAAGTAT

Alignment

ORF - retro_sscr_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVGVAHSEVNPNTRVMNSRGMWLTYALGVGLLHIVLLSIPFFSVPVAWTLTNVIHNLGMYVFLHAVKGTP
          NVG..H.EVNPNT.VMNSRGMWLTYALGVGLLHIVLLSIPF.SVPVAWTLTNVIH.LGMYVFLH.VKGTP
Retrocopy NVGISHREVNPNTWVMNSRGMWLTYALGVGLLHIVLLSIPFLSVPVAWTLTNVIHKLGMYVFLHTVKGTP

Parental  FETPDQGKARLLTHWEQLDYGVQFTSSRKFFTISPIILYFLASFYTKYDPTHFILNTASLLSVLIPKMPQ
          FETPDQGKA.LLTHWE..DYG.QFTSS.KFFTISPIILYFLASFYTKYDPTH.ILNT.SLLSVLI.KMPQ
Retrocopy FETPDQGKAKLLTHWE*SDYGIQFTSSWKFFTISPIILYFLASFYTKYDPTHLILNTTSLLSVLILKMPQ

Parental  LHGVRIFGINKY
          LHGV.IFGINKY
Retrocopy LHGVQIFGINKY

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	1.99 RPM
SRP014902_testis	0.00 RPM	23.06 RPM
SRP018288_heart	0.00 RPM	12.73 RPM
SRP018288_kidney	0.00 RPM	44.52 RPM
SRP018288_liver	0.00 RPM	46.37 RPM
SRP018288_lung	0.00 RPM	12.63 RPM
SRP018856_adipose	0.00 RPM	6.45 RPM
SRP035408_brain	0.00 RPM	10.48 RPM
SRP035408_liver	0.00 RPM	15.53 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_247 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_247 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005579	1 retrocopy	retro_cjac_2962,
Homo sapiens	ENSG00000128699	1 retrocopy	retro_hsap_645,
Gorilla gorilla	ENSGGOG00000015259	1 retrocopy	retro_ggor_565,
Loxodonta africana	ENSLAFG00000007769	1 retrocopy	retro_lafr_411,
Myotis lucifugus	ENSMLUG00000014339	1 retrocopy	retro_mluc_2318,
Macaca mulatta	ENSMMUG00000014316	1 retrocopy	retro_mmul_2432,
Nomascus leucogenys	ENSNLEG00000006625	1 retrocopy	retro_nleu_730,
Pongo abelii	ENSPPYG00000013017	2 retrocopies	retro_pabe_570, retro_pabe_571,
Pan troglodytes	ENSPTRG00000012736	1 retrocopy	retro_ptro_469,
Sus scrofa	ENSSSCG00000016044	1 retrocopy	retro_sscr_247 ,
Tupaia belangeri	ENSTBEG00000012942	1 retrocopy	retro_tbel_10,
Tursiops truncatus	ENSTTRG00000005240	2 retrocopies	retro_ttru_1846, retro_ttru_770,