RetrogeneDB ID: retro_rnor_2941

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:75176932..75177499(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000018301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HRAS1
• Ensembl ID: ENSRNOG00000016611
• Aliases: Hras, HRAS1, c-H-ras
• Description: GTPase HRas GTPase HRas, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:P20171]

Sequence

>retro_rnor_2941
ATGACAGAATACAAGCTTGTGGTGGTGGGTGCTGGAGGCGTGGGAAAGAGTGCCCTGACCATCCAGCTGATCCAGAACCA
TTTTGTGGACGAGTATGATTCCACTATAGAGGACTCCTACCGGAAACAGGTAGTCATTGATGGGGAGACGTGTTTAATGG
ACATCTTAGACACAGCAGGTCAAGAAGAGTATAGTGCCATGCGGGACCAGTACATGCGCACAGGGAAGGGCTTCCTCTGT
GTATTTGCCATCAACAACACCAAGTCCTTTGAAGACATACATCAGTACAGGGAGCAGATCAAGCGGGTGAAAGATTCAGA
TGATGTGCCTATGGTGCTGGTGGGCAACAAGTGTGACCTGGCCGCTCGCACTGTTGAGTCTCGGCAGGCCCAGGACCTTG
CTCGCAGCTATGGCATCCCCTACATTGAAACATCAGCCAAGACCCGGCAGGGTGTGGAGGATGCCTTCTACACACTAGTA
CGTGAGATTCGGCAGCATAAACTGCGGAAACTGAACCCGCCTGATGAGAGTGGCCCTGGCTGCATGAGCTGCACGTGTGT
GCTGTCC

Alignment

ORF - retro_rnor_2941 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
          MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYD.TIEDSYRKQVVIDGETCL.DILDTAGQEEYSAMRDQ
Retrocopy MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDSTIEDSYRKQVVIDGETCLMDILDTAGQEEYSAMRDQ

Parental  YMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIP
          YMRTG.GFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIP
Retrocopy YMRTGKGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIP

Parental  YIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
          YIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSC.CVLS
Retrocopy YIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCTCVLS

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	0.22 RPM	61.18 RPM
SRP017611_kidney	0.00 RPM	27.22 RPM
SRP017611_liver	0.13 RPM	18.76 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2941 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2941 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015293	3 retrocopies	retro_dnov_1358, retro_dnov_154, retro_dnov_2354,
Echinops telfairi	ENSETEG00000019899	2 retrocopies	retro_etel_1028, retro_etel_391,
Macropus eugenii	ENSMEUG00000008467	1 retrocopy	retro_meug_852,
Microcebus murinus	ENSMICG00000006472	1 retrocopy	retro_mmur_948,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Rattus norvegicus	ENSRNOG00000016611	1 retrocopy	retro_rnor_2941 ,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,