RetrogeneDB ID: retro_sscr_482

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:154126715..154127117(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000022358
• Aliases: None
• Description: ras-related protein Rab-28 [Source:RefSeq peptide;Acc:NP_001116647]

Sequence

>retro_sscr_482
CTGTCGGACTCCAAGGAGGAGAGCCAGCACCAGCAACAACTGAAAATTGGCGTGCTGGGGGACGGCACCTCCGGGAAGCC
CTCCTTAGCTGCGTGTTTTGCTCAAGAAACTTTTGGGAAACAGCACAAATGGACTCTAGGACTGGCTTTCTTTTTGAGAA
GGATAACATTGCCAGGAAACTGGACTCTTACTCTTCCAGTTTGAGACTTGGGAGGACAGACAACTGGAGGCAAGATGCTG
GGTAAGTAGATCTGCGGAGCACAGGGACTCCTCCTGGTAGGTGATATTACAAATTATCAGAGCTTCGAGAACTCAGAAGA
TTGGTATTCTGTGGTGCAGAAAGTGAGTGAGGAGTCGGAAACTCAGCCACTGGTTGCCTTGGTAGGCAATAAAATTGATT
TG

Alignment

ORF - retro_sscr_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 95.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDSEEESQ-DRQLKIVVLGDGTSGKTSLATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQVWDI
          .SDS.EESQ...QLKI.VLGDGTSGK.SLA.CFAQETFGKQ.K.T.GL.FFLRRITLPGN...TL.V.D.
Retrocopy LSDSKEESQHQQQLKIGVLGDGTSGKPSLAACFAQETFGKQHKWTLGLAFFLRRITLPGNWTLTLPV*DL

Parental  GGQTIGGKMLDKYIYGAQGILLVYDITNHQSFENLEDWYSVVKKVSEESETQPLVALVGNKSKL
          GGQT.GGKML.K.I.GAQG.LLV.DITN.QSFEN.EDWYSVV.KVSEESETQPLVALVGNK..L
Retrocopy GGQTTGGKMLGK*ICGAQGLLLVGDITNYQSFENSEDWYSVVQKVSEESETQPLVALVGNKIDL

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	3.98 RPM
SRP014902_testis	0.00 RPM	15.28 RPM
SRP018288_heart	0.00 RPM	11.11 RPM
SRP018288_kidney	0.00 RPM	12.81 RPM
SRP018288_liver	0.00 RPM	8.00 RPM
SRP018288_lung	0.00 RPM	13.85 RPM
SRP018856_adipose	0.00 RPM	7.61 RPM
SRP035408_brain	0.00 RPM	10.07 RPM
SRP035408_liver	0.00 RPM	10.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_482 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_482 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009344	1 retrocopy	retro_amel_469,
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771, retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482 , retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,
Tursiops truncatus	ENSTTRG00000003622	1 retrocopy	retro_ttru_697,