RetrogeneDB ID: retro_sscr_94

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:21509540..21510023(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000017446
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025528
• Aliases: None
• Description: None

Sequence

>retro_sscr_94
ATGCAGGCGGCGGATGCAGCACGCCCTGGACACATCACGCAGAGCAGCACGGCGGGAGGCCCCGAGGGCCCGGGCTGCAG
AGGTGGCCCAGGCGGCCCCAGCAGCCCCCGCGGTGATGGCTGCGTTGCTGCTGATGCAGCCGAGGGAGTTCCGCCTGTGG
CGCCAGGATGGCACCCTTCGGCAGCGGGCGGAGAGTCCGCATCCACAGCCAAAAGGCCAGGGAACCGACCACTCGTATTC
ACCCTAAGCGTACCTTTTCCGTCTTCCTTGGAGGCAGAGATCGCCCGTGGCTCCCTGGCCCCAGATGCTGAACCCCACCG
AGGGGCGGCTGGGAAGAAGCTCTCAGTGAGCGCCAGCGTCCTGGCCGTCCACTGGAGAGCTGAAGATTCCCGCCTCCTCC
GAATTTCCATCCTAAACTTCCTTGACCAGCTTTCCCTGGCGATTCGCACCATGCAGCGCTTTGGGCCCCCTGTTATCCGC
TAA

Alignment

ORF - retro_sscr_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.66 %
• Parental protein coverage: 93.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGAAGGSEGPGRRGAPGGRGRPRGAGA-AAVAAAGVPPVAPAQRTSEEGGDPASAAKRPRSRAHVFALSV
          S..AGG.EGPG.RG.PGG...PRG.G..AA.AA.GVPPVAP....S..GG..AS.AKRP..R..VF.LSV
Retrocopy SSTAGGPEGPGCRGGPGGPSSPRGDGCVAADAAEGVPPVAPGWHPSAAGGESASTAKRPGNRPLVFTLSV

Parental  PFPSSWEAEIARGSLAPDAEPHRGAVGKELTVSGSDLAVHWRADDSRLLRISIVNFLDQLSLVIRTMQRF
          PFPSS.EAEIARGSLAPDAEPHRGA.GK.L.VS.S.LAVHWRA.DSRLLRISI.NFLDQLSL.IRTMQRF
Retrocopy PFPSSLEAEIARGSLAPDAEPHRGAAGKKLSVSASVLAVHWRAEDSRLLRISILNFLDQLSLAIRTMQRF

Parental  GPPVSR
          GPPV.R
Retrocopy GPPVIR

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	27.87 RPM	24.82 RPM
SRP014902_testis	20.23 RPM	49.36 RPM
SRP018288_heart	0.21 RPM	7.07 RPM
SRP018288_kidney	0.99 RPM	12.61 RPM
SRP018288_liver	0.00 RPM	8.16 RPM
SRP018288_lung	9.37 RPM	7.54 RPM
SRP018856_adipose	3.87 RPM	15.30 RPM
SRP035408_brain	2.16 RPM	11.97 RPM
SRP035408_liver	0.18 RPM	8.25 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_94 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_94 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_94 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94 ,