RetrogeneDB ID: retro_rnor_474

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:123503321..123503895(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrpb
• Ensembl ID: ENSRNOG00000006961
• Aliases: None
• Description: small nuclear ribonucleoprotein-associated protein B [Source:RefSeq peptide;Acc:NP_599185]

Sequence

>retro_rnor_474
ATGACTGTGGGCAAGAGCAACAATATGCTGCAGCACATTAGCTACTGGATGAGCAGCATCCTGAAAAATGGCTGGTTCTT
TATTGGACCTTCAAGACATTTGACAAGCATATGAATTTGATCCTCTGTGGTCGTGATGAGTTCAGGGAGATCAGGCTAAA
GAACTCCAAACAATCAGAAAGAGAAGAGAAGCTAGTCCTTGTTCTTTTGTTCCTTTAAGGGAGAATTCTGGTCTTCAAGA
AAGTAGAAGGATCTCCTCCTCTTAAAGATACTGGCATTGCCTGAGTGCAACTTGCTGGAGATACCAAATGGCCAGGTATT
CACGAGTATGCTGGCAGAGGAATCCCAGCTAGTGTTCCTATGCTCCCAGGCTCCTGTAGAACTTTCTGGGCTAGTATGAA
ATGTTGGAGGGTCATTTCAGCAGATAATGACCCCACAAGGAAGAGGTACCGTTGGCAGCTGCTAGAGCTGCAGCCACAGC
CATTGTTGTAGGAGCACCATCTCAGTACTCCTCTGGTCATGGGTTTCCTCCTATGATGGGTCCACCTGGCAAGAAACAGC
CCATGGGTGCCCCA

Alignment

ORF - retro_rnor_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 83.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVGKSSKMLQHIDYRMRCILQDGRIFIG-TFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGL
          MTVGKS..MLQHI.Y.M..IL..G..FIG.TFK.FDKHMNLILC..DEFR.I..KNSKQ.EREEK.VL.L
Retrocopy MTVGKSNNMLQHISYWMSSILKNGWFFIG<TFKTFDKHMNLILCGRDEFREIRLKNSKQSEREEKLVLVL

Parental  VLLRGENLVSMTVEGPPP-KDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM-PQAPAGLAGPVRGVGGP
          ..L.G..LV...VEG.PP.KDTGIA.V.LAG....PGI...AGRGIPA.VPM..QAP..L.G.V..VGG.
Retrocopy LFL*GRILVFKKVEGSPPLKDTGIA*VQLAGDTKWPGIHEYAGRGIPASVPM>SQAPVELSGLV*NVGGS

Parental  SQQVMTPQGRGTV-AAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPP
          .QQ.MTPQGRGTV.AAA.AAATA...GAP.QY..G.G.PP.....G...P..MG.P
Retrocopy FQQIMTPQGRGTV>AAARAAATAIVVGAPSQYSSGHGFPPMMGPPGKKQP--MGAP

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	0.14 RPM	22.86 RPM
SRP017611_kidney	0.00 RPM	69.71 RPM
SRP017611_liver	0.00 RPM	24.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_474 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938, retro_mmus_3450, retro_mmus_554,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474 ,
Rattus norvegicus	ENSRNOG00000015976	6 retrocopies	retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,