RetrogeneDB ID: retro_rnor_2729

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:41184089..41184439(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrpd1
• Ensembl ID: ENSRNOG00000013714
• Aliases: None
• Description: small nuclear ribonucleoprotein Sm D1 [Source:RefSeq peptide;Acc:NP_001099633]

Sequence

>retro_rnor_2729
ATGAAGCTCGTGAGATTTTTGATGAAATCGAGTCATGAAACTGTAACCATTGAATTGAAGAATGGAACGCAAGTCCATGG
AACAATCGCAGGTGTAGATGTCAGCATGAATACGCACCTTAAAGCTGTGAAAATGGCCCTGAAGAACAGAGATCCTGTAC
AGGTGGAAACATTGAGTATTTGAGGCAATAACATTCGGCATTTTATTCCACCAGACAGCTTACCTCTAGATACACTACTT
GTGGTTCTAAGGTGAAATCTAAGAAAAGAGAAGCTGTTGCAGGAAGAGGCAGAGGCGGGGGTAGAGGGAGAAGACGCTTT
CGCGGCAGAGGAAGAGGGCGCCCTAGGCGA

Alignment

ORF - retro_rnor_2729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL
          MKLVRFLMK.SHETVTIELKNGTQVHGTI.GVDVSMNTHLKAVKM.LKNR.PVQ.ETLSI.GNNIR.FI.
Retrocopy MKLVRFLMKSSHETVTIELKNGTQVHGTIAGVDVSMNTHLKAVKMALKNRDPVQVETLSI*GNNIRHFIP

Parental  PDSLPLDTLLVDV-EPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
          PDSLPLDTLLV.....K.K.....A..GRG.GRGR.R.RGRGRGR..PRR
Retrocopy PDSLPLDTLLVVL<KVKSKKREAVAGRGRGGGRGRRRFRGRGRGR--PRR

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
SRP017611_brain	0.00 RPM	14.81 RPM
SRP017611_kidney	0.00 RPM	6.00 RPM
SRP017611_liver	0.00 RPM	2.02 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2729 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2729 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729 ,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,