RetrogeneDB ID: retro_rnor_2173

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:136459499..136460720(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000023004
• 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_2173
GCGGCGGCGATGACCGGGGAGAAGATCCTCTCCCTGCGGAGGGACCACAAACCCAGCAAAGAGGACGGGGACGTGCTGGA
GCCCTGCGAGGAGGAGGCGACGGCCGCGCTCGGCGGCGCCTTCACCGGGGGCAGAAGCGGAGCAGGCGGCAGCGGCAAGG
GCGGCAAGGCCTGCCATAAGATCTTCAGCCACCACCACCGGCTGCAGCTGAAGGCGCCCGCTGCGCCCGGCCCCGGCATT
CCGGCCCCGCCGCAGCACAACGCAGTGACTGCCACCTGCCCGGCTCCGGCCTGCCTGGGCAGTAACCCGGTTGTGGTGGC
TGACGGAGGCAGCTGCCCCTCGCTCTACCCGGTGCACGAGTGCGTCTTTAAGGGGGACGTGAGGAGACTGTCCTCGCTTA
TCCGCACGCACAATATCGGACAGAAAGATAATCACGGAAACACTCCTTTACATCTTGCTGTGATGTTAGGAAATAAAGAA
TGTGCACATTTACTGTTGGCTCACAATGCTCCAGTAAAGGTGAAAAATGCTCAGGGATGGAGCCCTCTGGCGGAAGCCAT
CAGCTATGGAGACAGACAGATGATCACAGCTCTTCTAAGGAAACTCAAGCAGCAATCTAGGGAGAGTGTTGGAGAAAAAC
GACCTCGGTTGTTAAAAGCCCTAAAAGAGTTAGGTGACTTTTACCTAGAACTTCACTGGGATTTTCAAAGCTGGGTGCCT
TTGCTTTCCCGAATTCTGCCTTCTGATGCCTGTAAAATATACAAGCAAGGTATCAATATCAGGCTTGACACAACTCTCAT
AGACTTTACTGACATGAAGTGCCAACGAGGGGACCTGAGCTTCATCTTCAGTGGGGATGCTGCACCCTCTGAGTCTTTTG
TAGTGTTAGACAATGAACAAAAAGTTTATCAGCGAATACACCATGAGGAGTCAGAGATGGAAACAGAAGAGGAAGTTGAT
ATTTTAATGAGCAGCGATATTTATTCTGCAACTTTATCAACCAAATCAATTTCTTTCACACGTGCCCAAACTGGATGGCT
TTTTCGGGAAGATAAAACAGAAAGAGTAGGAAACTTTTTGGCAGACTTTTATCTGGTGAATGGACTTGTTCTAGAATCAA
GGAAAAGAAGAGAGCACCTTAGCGAGGAGGACATTCTGCGGAATAAGGCCATCATGGAGAGCCTGAGCAAAGGTGGGAGC
CTGACGGAGCAGAACTTTGAG

Alignment

ORF - retro_rnor_2173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.77 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARRMTGEKIRSLRRDHKPSKEDGDVLEPCEEEATAALGGAFTGGRSGAGGSGKGGKACHKIFSHHHRLQL
          A..MTGEKI.SLRRDHKPSKEDGDVLEPCEEEATAALGGAFTGGRSGAGGSGKGGKACHKIFSHHHRLQL
Retrocopy AAAMTGEKILSLRRDHKPSKEDGDVLEPCEEEATAALGGAFTGGRSGAGGSGKGGKACHKIFSHHHRLQL

Parental  KAPTAPGPGVPAPPQHNAVTATCPAPACLGSNPVVVADGGSCPSLYPVHECVFKGDVRRLSSLIRTHNIG
          KAP.APGPG.PAPPQHNAVTATCPAPACLGSNPVVVADGGSCPSLYPVHECVFKGDVRRLSSLIRTHNIG
Retrocopy KAPAAPGPGIPAPPQHNAVTATCPAPACLGSNPVVVADGGSCPSLYPVHECVFKGDVRRLSSLIRTHNIG

Parental  QKDNHGNTPLHLAVMLGNKECAHLLLAHNAPVKVKNAQGWSPLAEAISYGDRQMITALLRKLKQQSRESV
          QKDNHGNTPLHLAVMLGNKECAHLLLAHNAPVKVKNAQGWSPLAEAISYGDRQMITALLRKLKQQSRESV
Retrocopy QKDNHGNTPLHLAVMLGNKECAHLLLAHNAPVKVKNAQGWSPLAEAISYGDRQMITALLRKLKQQSRESV

Parental  GEKRPRLLKALKELGDFYLELHWDFQSWVPLLSRILPSDACKIYKQGINIRLDTTLIDFTDMKCQRGDLS
          GEKRPRLLKALKELGDFYLELHWDFQSWVPLLSRILPSDACKIYKQGINIRLDTTLIDFTDMKCQRGDLS
Retrocopy GEKRPRLLKALKELGDFYLELHWDFQSWVPLLSRILPSDACKIYKQGINIRLDTTLIDFTDMKCQRGDLS

Parental  FIFSGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDILMSSDIYSATLSTKSISFTRAQTGWLFRE
          FIFSGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDILMSSDIYSATLSTKSISFTRAQTGWLFRE
Retrocopy FIFSGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDILMSSDIYSATLSTKSISFTRAQTGWLFRE

Parental  DKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIMESLSKGGSLTEQNFE
          DKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIMESLSKGGSLTEQNFE
Retrocopy DKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIMESLSKGGSLTEQNFE

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	1.26 RPM	81.09 RPM
SRP017611_liver	0.20 RPM	19.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2173 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2173 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 ,