RetrogeneDB ID: retro_rnor_450

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:75299417..75301286(+)
• Located in intron of: ENSRNOG00000027855

Retrocopy information

• Ensembl ID: ENSRNOG00000018600
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Txndc11
• Ensembl ID: ENSRNOG00000002452
• Aliases: Txndc11, RGD1307538
• Description: thioredoxin domain-containing protein 11 [Source:RefSeq peptide;Acc:NP_001121004]

Sequence

>retro_rnor_450
ATATCAGAATGCGGAGGCTTTGGCGGCGGCGGCAGAAACAACAGCGAGGACGCTGAGGACAAGGGTGGCGGCCCCCAGCT
CCCTCAGCCCTGCCCGGGCGGCGGCGTCCTCAGAGGGCAGGATCCGCCGCGAATTGCACGGCGCCTTGCTTATGGCGTGC
CAGCGGCCGGAGCTACTGTGCAGTTCCCTGGCTCTCGGCTGTGCCCTGCTCTTCGCCCTCAAGTTCACCTGCAGTCGAGC
CAAAGACGTGGTAATACCAGCAAAGCCGCCTGTCAACCTTTTCTCCTCGAGGTCTCCAGTCCTTGACCTCTTCCAGGGGC
AGATGGACTACGCTGACCATGTCCGCCAGGATTCTGAGGTGGTGGTGCTGTTCTTCTATGCCCCATGGTGCGGCCAGTCC
ATTGCTGCCAGGGCAGAAATTGAGCAGGCAGCCAGCCGGCTTTCAGATCAGGTATTGTTCGTGGCAGTAAACTGTTGGTG
GAACCAGGGGGAATGCAGAAAACAGAAGCATTTCTTCTACTTCCCTGTGATACATCTGTATCATCGGAGTCTTGGACCAA
TTGAATACAAAGGCCCCATGAGTGCTGTTTAACATTGAGAAGTTTGTTCGCCAGGTGATGAAACCTCTTCTCTATATCCC
ATCTCAATCAGAATTGCTAGATTTTCTCTCCAACTATGAGCCTGAAGTACTCGGCTACTTCGAATTCAGTGGTTCTCCCC
AGTCTCCTGGATACTTGACCTTCTTCACCTCAGCACTGCACTCTTTAAAGAAAGATTACCTAGGAACAGTACGATTTGGA
ACAGAACAAATAAACATCTTGCGAAACTGGTATCCTTAGCACACTCTGGAAGTGTGTATTTACATAGACATTTCAACACA
TCATTTGTCTTCCCCAGGGAAGTCATGAACTTCACAGCTGAGAACATCTATAAGTGGGCCTCAGAAAACCAGGAGACCCT
CTTCCGATGGCTACAACCCCATGGAGGCAAGAGTCTGCTGTTGAACAATGAGCTGAAGAAAGGACCAGCACTCTTCCTGC
TCACACCTTTTGATCCCTTAGCCGAGAGGCATCCTCTCCTAGATGAGATCACCGAAGTGGCCTTGGAGTACAGTAACTGT
CGTGGGGACCAGGTGGTGGAGCGCCTCCTTCAGCACCTGCAGCGGGGAGAAGCACCCGTGTTCCAGTCCCTGGCACCAGA
GCTGCAAGCCCCTCTGCCTGATACTGAGCTGATGGCAGCGTCCCCCTGCTGTAACACAGTGGTGCTGCCACAGGGGCCAG
CCCTCTCCAGGACCCACAATGTCTGTGAGCTGTGTGTCAACCAGTCAGTGGGTACCAGGCCTAGCTCAGTGAGTGTGCCA
CAGTGCAGCTTCTTCGAGATGGCAGCCGCTCTGGATTCTTTCTACCTCAAGGAGCAGACTTTTTATCGTGTGGTGTCAGG
CAGCATAGAATGCAGCAATTATTTAACCTCCTATAGTCCTTTCAGCTTCTACACTGCATGTTGCAGGACTATATCCCGGG
GCACGACAAGTTTCTCTGGCTCTGCACAGGACGTCTTCACAGCCCCAGCCATCGAATTCTCTGCCTTAGAGAAAGAGCTG
CTGCCCGAGCTCCATTCCTCACATTGAGGAGAATAGGTACCACTTTCCTGAAGTGGGCCTCTCTAGCACAGCCTTCACAG
GCCTGAGCTGCAGAACCAACAAGACTCTGAACATCTACCTTTTGGATTCCAATTTATTTTGGTTATATGCAGAGAGACTG
GATGCCCCCAAGCTCTGCTCCCGTGAAGGAGTTTGCCACAATTGTCGATGTGAAAGAAGAATCTCACTATATCCTGGATC
CCAAACAAGCCCTCATGAAGTTCACTCTG

Alignment

ORF - retro_rnor_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.21 %
• Parental protein coverage: 66.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSECGGRGGGGGNNSEDAEDEGGGPKGS-GSLSPAGAAASSEGRIRRGLRGASLMARQRPELLCGAVALG
          .SEC...GG.GG......ED......G...SLSPA.AAASSEGRIRR.L.GA.LMA.QRPELLC...ALG
Retrocopy ISEC---GGFGGGGRNNSEDAEDKGGGP>SSLSPARAAASSEGRIRRELHGALLMACQRPELLCSSLALG

Parental  CALLFALKFTCSRAKDVIIPAKPPVSFFSSRSPVLDLFQGQLDYADHVRQDSEVVVLFFYAPWCGQSIAA
          CALLFALKFTCSRAKDV.IPAKPPV..FSSRSPVLDLFQGQ.DYADHVRQDSEVVVLFFYAPWCGQSIAA
Retrocopy CALLFALKFTCSRAKDVVIPAKPPVNLFSSRSPVLDLFQGQMDYADHVRQDSEVVVLFFYAPWCGQSIAA

Parental  RAEIEQAASRLSDQVLFVAVNCWWNQGKCRKQKHFFYFPVIHLYHRSFGPIEYKGPMSAV-YIEKFVRRV
          RAEIEQAASRLSDQVLFVAVNCWWNQG.CRKQKHFFYFPVIHLYHRS.GPIEYKGPMSAV..IEKFVR.V
Retrocopy RAEIEQAASRLSDQVLFVAVNCWWNQGECRKQKHFFYFPVIHLYHRSLGPIEYKGPMSAV>NIEKFVRQV

Parental  MKPLLYIPSQSELLDFLSNYEPGVLGYFEFSGSPQPPGYLTFFTSALHSLKKDYLGTVRFGVI-TNKHLA
          MKPLLYIPSQSELLDFLSNYEP.VLGYFEFSGSPQ.PGYLTFFTSALHSLKKDYLGTVRFG...TNKHLA
Retrocopy MKPLLYIPSQSELLDFLSNYEPEVLGYFEFSGSPQSPGYLTFFTSALHSLKKDYLGTVRFGTE<TNKHLA

Parental  KLVSLVHSGSVYLHRHFNTSLVFPREVMNFTAENIYKWASENQETLFRWLQPHGGKSLLLNNELKKGPAL
          KLVSL.HSGSVYLHRHFNTS.VFPREVMNFTAENIYKWASENQETLFRWLQPHGGKSLLLNNELKKGPAL
Retrocopy KLVSLAHSGSVYLHRHFNTSFVFPREVMNFTAENIYKWASENQETLFRWLQPHGGKSLLLNNELKKGPAL

Parental  FLFIPFDPLAERHPLLDEITEVALEYSNCRGDQVVERLLQHLRRAEAPVFQSLAPELQAPLPDAQLMAAS
          FL..PFDPLAERHPLLDEITEVALEYSNCRGDQVVERLLQHL.R.EAPVFQSLAPELQAPLPD..LMAAS
Retrocopy FLLTPFDPLAERHPLLDEITEVALEYSNCRGDQVVERLLQHLQRGEAPVFQSLAPELQAPLPDTELMAAS

Parental  PCCNTVVLPQGPALSRTHNVCELCVNQSVGTRPSSVSVPQCSFFEMAAALDSFYLKEQTFYRVVSGSIEC
          PCCNTVVLPQGPALSRTHNVCELCVNQSVGTRPSSVSVPQCSFFEMAAALDSFYLKEQTFYRVVSGSIEC
Retrocopy PCCNTVVLPQGPALSRTHNVCELCVNQSVGTRPSSVSVPQCSFFEMAAALDSFYLKEQTFYRVVSGSIEC

Parental  SNFLTSYSPFSFYTACCRTISRGTASFSGSAQDVFTAPAIEFSALE-KSCEATAPSSIPHIEENRYRFPE
          SN.LTSYSPFSFYTACCRTISRGT.SFSGSAQDVFTAPAIEFSALE.KSC....PSSIPHIEENRY.FPE
Retrocopy SNYLTSYSPFSFYTACCRTISRGTTSFSGSAQDVFTAPAIEFSALE>KSC---CPSSIPHIEENRYHFPE

Parental  VGLSSTAFTGLSCRTNKTLNIYLLDSNLFWLYAERLGA-PSSAPVKEFATIVDVKEESHYILDPKQALVK
          VGLSSTAFTGLSCRTNKTLNIYLLDSNLFWLYAERL.A.PSSAPVKEFATIVDVKEESHYILDPKQAL.K
Retrocopy VGLSSTAFTGLSCRTNKTLNIYLLDSNLFWLYAERLDA>PSSAPVKEFATIVDVKEESHYILDPKQALMK

Parental  LTL
          .TL
Retrocopy FTL

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	25.74 RPM
SRP017611_kidney	0.00 RPM	37.75 RPM
SRP017611_liver	0.00 RPM	48.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_450 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_450 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000002452	1 retrocopy	retro_rnor_450 ,