RetrogeneDB ID: retro_rnor_2098

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:211475004..211475877(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000026718
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ankrd13c
• Ensembl ID: ENSRNOG00000011340
• Aliases: None
• Description: ankyrin repeat domain-containing protein 13C [Source:RefSeq peptide;Acc:NP_001178499]

Sequence

>retro_rnor_2098
ATATACAAGCAAGGTATCAATATCAGGCTTGACACAACTCTCATAGACTTTACTGACATGAAGTGCCAACGAGGGGATCT
AAGCTTCATCTTCAATGGGGATGCTGCACCCTCTGAGTCTTTCGTAGTGTTAGACAATGAACAAAAAGTTTATCAGCGAA
TACACCATGAGGAGTCAGAGATGGAAACAGAAGAGGAAGTTGATATTTTAATGAGCAGCAATATTTATTCTGCAACTTTA
TCAACCAAATCAATTTCTTTCACACGTGCCCAAACTGGATGGCTTTTTCGGGAAGATAAAACAGAAAGAGTAGGAAACTT
TTTGGCAGACTTTTATCTGGTGAATGGACTTGTTCTAGAATCAAGGAAAAGAAGAGAGCACCTTAGCGAGGAGGACATTC
TGCGGAATAAGGCCATCATGGAGAGCCTGAGCAAAGGTGGGAGCCTGACGGAGCAGAACTTTGAGCCGGTTAGAAGACAG
TCTCTTACCCCTCCTCCTCAGAACACTATTACGTGGGAAGAATACATATCTGCTGAAAATGGAAAGGCACCACACCTGGG
CAGAGAACTGGAGTGCAAAGAGAGCAAGAAGACATTTAAAGCCACTGTAGCCATGAGCCAGGAATTTCCTCTGGGAATTG
AGTCATTATTGAATGTTCTAGAAGTAATAGCACCCTTCAAGCACTTTAACAAGCTTAGAGAATTTGTTCAAATGAAGCTT
CCTCCTGGCTTTCCTGTAAAATTAGATATACCCGTGTTTCCCATGATCACAGCCACTGTGACTTTTCAGGAATTCCGATG
TGATGAATTTGATGGGTCCATCTTTGCCATCCCTGAAGACTACAAGGAAGACCCAAGTCGTTTTCCTGACCTT

Alignment

ORF - retro_rnor_2098 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.63 %
• Parental protein coverage: 52.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IYKQGINIRLDTTLIDFTDMKCQRGDLSFIFSGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDIL
          IYKQGINIRLDTTLIDFTDMKCQRGDLSFIF.GDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDIL
Retrocopy IYKQGINIRLDTTLIDFTDMKCQRGDLSFIFNGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDIL

Parental  MSSDIYSATLSTKSISFTRAQTGWLFREDKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIM
          MSS.IYSATLSTKSISFTRAQTGWLFREDKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIM
Retrocopy MSSNIYSATLSTKSISFTRAQTGWLFREDKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIM

Parental  ESLSKGGSLTEQNFEPVRRQSLTPPPQNTITWEEYISAENGKAPHLGRELVCKESKKTFKATVAMSQEFP
          ESLSKGGSLTEQNFEPVRRQSLTPPPQNTITWEEYISAENGKAPHLGREL.CKESKKTFKATVAMSQEFP
Retrocopy ESLSKGGSLTEQNFEPVRRQSLTPPPQNTITWEEYISAENGKAPHLGRELECKESKKTFKATVAMSQEFP

Parental  LGIESLLNVLEVIAPFKHFNKLREFVQMKLPPGFPVKLDIPVFPTITATVTFQEFRCDEFDGSIFAIPED
          LGIESLLNVLEVIAPFKHFNKLREFVQMKLPPGFPVKLDIPVFP.ITATVTFQEFRCDEFDGSIFAIPED
Retrocopy LGIESLLNVLEVIAPFKHFNKLREFVQMKLPPGFPVKLDIPVFPMITATVTFQEFRCDEFDGSIFAIPED

Parental  YKEDPSRFPDL
          YKEDPSRFPDL
Retrocopy YKEDPSRFPDL

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	46.30 RPM
SRP017611_kidney	0.70 RPM	81.09 RPM
SRP017611_liver	0.27 RPM	19.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2098 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2098 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
Gallus gallus	ENSGALG00000011311	1 retrocopy	retro_ggal_23,
Rattus norvegicus	ENSRNOG00000001204	1 retrocopy	retro_rnor_986,
Rattus norvegicus	ENSRNOG00000011340	2 retrocopies	retro_rnor_2098 , retro_rnor_2173,