RetrogeneDB ID: retro_rnor_782

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:11950004..11950588(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000030674
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Chmp6
• Ensembl ID: ENSRNOG00000004014
• Aliases: Chmp6, RGD1565325
• Description: charged multivesicular body protein 6 [Source:RefSeq peptide;Acc:NP_001099326]

Sequence

>retro_rnor_782
GGTCGCAAGAAGCAGAGCCGGGTCACCGAACAGGACAGGGCCATCCTGCAACTGAAGCAGCAGAGAGACAAGCTGAGGCA
GTACCAGAAGAGGGTCACGCAGCAGCTGGAGAGGGAAGGGGTTTGGCCAGGCAGCTGCTTCGGGATGGCAGGAAAGAACA
GGCCAAGCTGCTACTCAAGAAGAAGAGGTACCGGGAGCAACTGCTCGATAGGACAGAAAACCAGATCAGCAGCCTGGAAG
CCATGGTTCAGAGCATTGAGTTCATGCAGATCGAGATGAAGGTGATGGAGGGGCTTCAGGTGGGGAACGAATGTCTGAAT
AAGATGCACCAGGTGATGTCCATAGAGGAGGTGGAGAGGATCCTGGACGAGACCCAGGAGGCCGTGGAGTACCAGCGGCA
AATTGATGAGCTGCTGGCAGGAAGTTTCACCCAGGAGGACGAGGATGCCATCCTGGAAGAGCTGAATGCAATCACTCAGG
AACAAATCGAGTTACCAGAGGTTCCTTCAGAGTCCCTGCCTGACACAAGCCCAGAAGCCCCTGCCAAGGCCAGATCCAGG
CAGGCAGAGCTGGTGGCCGCTTCG

Alignment

ORF - retro_rnor_782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.45 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRKKQSRVTEQDRAILQLKQQRDKLRQYQKRVTQQLERE-RALARQLLRDGRKERAKLLLKKKRYREQLL
          GRKKQSRVTEQDRAILQLKQQRDKLRQYQKRVTQQLERE.R.LARQLLRDGRKE.AKLLLKKKRYREQLL
Retrocopy GRKKQSRVTEQDRAILQLKQQRDKLRQYQKRVTQQLERE<RGLARQLLRDGRKEQAKLLLKKKRYREQLL

Parental  DRTENQISSLEAMVQSIEFTQIEMKVMEGLQVGNECLNKMHQVMSIEEVERILDETQEAVEYQRQIDELL
          DRTENQISSLEAMVQSIEF.QIEMKVMEGLQVGNECLNKMHQVMSIEEVERILDETQEAVEYQRQIDELL
Retrocopy DRTENQISSLEAMVQSIEFMQIEMKVMEGLQVGNECLNKMHQVMSIEEVERILDETQEAVEYQRQIDELL

Parental  AGSFTQEDEDAILEELNAITQEQIELPEVPSEPLPDTSPEAPAKARSRQAELVAAS
          AGSFTQEDEDAILEELNAITQEQIELPEVPSE.LPDTSPEAPAKARSRQAELVAAS
Retrocopy AGSFTQEDEDAILEELNAITQEQIELPEVPSESLPDTSPEAPAKARSRQAELVAAS

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	19.99 RPM
SRP017611_kidney	0.07 RPM	22.75 RPM
SRP017611_liver	0.00 RPM	7.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_782 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_782 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003320	2 retrocopies	retro_meug_1370, retro_meug_762,
Mus musculus	ENSMUSG00000025371	1 retrocopy	retro_mmus_2033,
Rattus norvegicus	ENSRNOG00000004014	1 retrocopy	retro_rnor_782 ,