RetrogeneDB ID: retro_rnor_887

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:10914253..10914614(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dusp22
• Ensembl ID: ENSRNOG00000018218
• Aliases: None
• Description: dual specificity phosphatase 22 [Source:RefSeq peptide;Acc:NP_001101882]

Sequence

>retro_rnor_887
ACGCGGAACAAGGTGACACACATTCTTCCTGTGCATGACACTGCCAGGCCCATGCTGGAGGGAGTTAAATAGCTGTGTAT
TCCAGCAGCAGCCTCACCGGCTCAAAACCTGACAAGACATCTCAAAGAAAGTATTAAATTCCTTCATGAGTGCCGACTCC
AGGGTGAGGGCTGACTTGTGCATTGCCTGGCGGGGGTCTCCGGGAGTGTGACACTGGTGATCGCATACATCATGACTGTC
ACCGACTGTGGCTGGGAAGAGGCCTTGCACGCCGTTCGTTCGTGCGGGGAGGTCCTGTGCTAACCCCAACCTGGGCTTCC
AAAGGCAGCTGCAGGAGTCTGAGAAACACGAAGTGAGGCAG

Alignment

ORF - retro_rnor_887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 64.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRNKVTHILSVHDTARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLQGEGCLVHCLAGVSRSV
          .RNKVTHIL.VHDTARPMLEGVK.LCIPAA.SP.QNLTRH.KESIKF.HECRLQGEG.LVHCLAGVS.SV
Retrocopy TRNKVTHILPVHDTARPMLEGVK*LCIPAAASPAQNLTRHLKESIKFLHECRLQGEG*LVHCLAGVSGSV

Parental  TLVIAYIMTVTDFGWEEALHTVRA-GRSCANPNLG-FQRQLQEFEKHEVRQ
          TLVIAYIMTVTD.GWEEALH.VR..G.....P..G.FQRQLQE.EKHEVRQ
Retrocopy TLVIAYIMTVTDCGWEEALHAVRSCGEVLC*PQPG>FQRQLQESEKHEVRQ

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	8.84 RPM
SRP017611_kidney	0.00 RPM	9.07 RPM
SRP017611_liver	0.00 RPM	6.66 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_887 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_887 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011289	1 retrocopy	retro_etel_1581,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Rattus norvegicus	ENSRNOG00000018218	2 retrocopies	retro_rnor_858, retro_rnor_887 ,
Sarcophilus harrisii	ENSSHAG00000015165	2 retrocopies	retro_shar_241, retro_shar_310,
Tursiops truncatus	ENSTTRG00000001848	1 retrocopy	retro_ttru_668,