RetrogeneDB ID: retro_rnor_986

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:938389..940054(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ankrd13a
• Ensembl ID: ENSRNOG00000001204
• Aliases: Ankrd13a, Ankrd13
• Description: ankyrin repeat domain-containing protein 13A [Source:RefSeq peptide;Acc:NP_001012148]

Sequence

>retro_rnor_986
ATGTCCTCGGCCGGCGACACCAGTAGCCGCTTCCGGCTGCACCTTCTGTTCTGGAACAACTACTACAGGCAGCTGGAGAA
GGAGCTGTGGAGCCAGAATGCAGAAGCCTTGGATCCACAGGGTCGGACATTACTGCACCTTGCGGTTTCTCTGGGACATT
TGGAATCTACTCGAGTCTTGCTGCGACATAAAGCAGACATGACCAAAGAGAATGGCCAGGGATGGACAGTCTTACACGAA
GCTGTGAGCACAGAAGATCCCGAGATGGTGTACACAGTCCTGAAGCACCGAGACTACCACAACACAGCCATGGCCCTGGA
AGGTGTACCTGAGTTGCTACACAAAATTCTTGAGGCTCCGGATTTCTACATGCAATTGAAGTGGGAGTTCACCAGTTGGG
TGCCCTTGGTGTCCAGAATATGCCCCAACGACGGACGTGTGTCACGTCTGGAAGAGCGGGGCCAAGCTGTGCATGGACAT
CACCTTGCTGGGGTTTGAAAATATGAGCTGGATAAGAGGGAGGTGGAGTCTCATATTTAAGGGAGGAGATAACTGGGCAG
AGCTGATGGAGGTCAACCATGATGACCGTGTGGTCACCACCGAACACTTCGATCTTTCACAAGAAATGGAGCGCCTCATC
CTGGACCTGATAAAGCAAAAAAGCAGGGAGGTGGAGAGGGTGGTGGACAAGCCCTGTCATCAACACCAACTTCGATACTA
AGAACGTTGCCTTTGAAAGAACTAAATCCAAATTCTGGGAATGGAGGACAGATAAAGTGGAAGTTGTTAATGGCTACGAA
GCAAAGGTTTACTCGGTAAACAATGTGAGCATGATAACCAAGATCCGTACAGAGCACCTGATGGAGGAGGAGAAGAAGAG
ATAGAAAGAGGACCTGAATCCACTGGAGTCTCTGCTCAGAACTGTGGAACATCAGTTTGGTGCTCAAGGGGACCTCACTA
CAGAGTGTGCCACTGTGAACAGCCCCACGGCCATCATGTCCATTGAATACTTTGATGAAGACTTCGATCTGAAAGACCAG
GACATTGGAAGACCAAAGGAGCTGACGATTAGAACACAGAAGTTTAAAGCTACCCTGTGGATGTGCGAGGAGTTCCCGCT
CTCCCTTGTGGAGCAGGTCATCCCTATCATTGACCTCATGGCTCGCACCAGAGCTCACTTTGCAAGATTGAGAGATTTCA
TCAAATTGGACTTCCCTCCTGGATTTCCGGTCAAAATAGAAATCCCCTTAATTCCACGTCTTAAATGCGCGGATTATGTT
CGGAAATGTTAATGACTGCAGCACTGCTGAAGAGAGGCAGAGCGTGGAAGGGACCCAGGCTGAGTGTGCAGCTTCTGATG
CCACAGACTTCGAGGTTGATCAATCTGTATTTGAAATCCCTGCATTCTATCACGTTCAAGACAATGGCAGAAACGTGCAC
CTGCAAGACGAGGACTACGAGATCATGCAGTTCACCATTCAGCAGAGCCTGCTCGAGTCTAGCAGGAGCTAGGATCTTTT
AGGACCAGCTTCAAATGGAGGGATCAGCTACGCCCACAGTTATGAAGCCCAGTATGAGAGGGCCATCCAGGAGAGTCTCC
TAACTAACATGGAAGGCCGGTGCCCGGGTGGTCTCAGTGAGTCCAGCCGTTTCGATAGCGACCTG

Alignment

ORF - retro_rnor_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.87 %
• Parental protein coverage: 93.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSARDTSSRFPLHLLVWNNDYRQLEKELRDQNAEALDPRGRTLLHLAVSLGHLESARVLLRHKADVTKE
          MSSA.DTSSRF.LHLL.WNN.YRQLEKEL..QNAEALDP.GRTLLHLAVSLGHLES.RVLLRHKAD.TKE
Retrocopy MSSAGDTSSRFRLHLLFWNNYYRQLEKELWSQNAEALDPQGRTLLHLAVSLGHLESTRVLLRHKADMTKE

Parental  NGQGWTVLHEAVSTGDPEMVYTVLQHRDYHNTSMALEGVPELLHKILEAPDFYVQMKWEFTSWV-PLVSR
          NGQGWTVLHEAVST.DPEMVYTVL.HRDYHNT.MALEGVPELLHKILEAPDFY.Q.KWEFTSWV.P....
Retrocopy NGQGWTVLHEAVSTEDPEMVYTVLKHRDYHNTAMALEGVPELLHKILEAPDFYMQLKWEFTSWV>PWCPE

Parental  ICPN-DVCRIWKSGAKLRVDITLLGFENMSWIRGRRSLIFKGGDNWAELMEVNHDDRVVTTEHFDLSQEM
          ..P..DVC..WKSGAKL..DITLLGFENMSWIRGR.SLIFKGGDNWAELMEVNHDDRVVTTEHFDLSQEM
Retrocopy YAPTTDVCHVWKSGAKLCMDITLLGFENMSWIRGRWSLIFKGGDNWAELMEVNHDDRVVTTEHFDLSQEM

Parental  ERLTLDLMKPKSREVERRL-TSPVINTSLDTKNVAFERTKSGFWGWRTDKAEVVNGYEAKVYSVNNVSVI
          ERL.LDL.K.KSREVER...TSPVINT..DTKNVAFERTKS.FW.WRTDK.EVVNGYEAKVYSVNNVS.I
Retrocopy ERLILDLIKQKSREVERVV>TSPVINTNFDTKNVAFERTKSKFWEWRTDKVEVVNGYEAKVYSVNNVSMI

Parental  TKIRTEHLTEEEKKRYKEDRNPLESLLGTVEHQFGAQGDLTTECATVNNPTAITPDEYFDEDFDLKDRDI
          TKIRTEHL.EEEKKR.KED.NPLESLL.TVEHQFGAQGDLTTECATVN.PTAI...EYFDEDFDLKD.DI
Retrocopy TKIRTEHLMEEEKKR*KEDLNPLESLLRTVEHQFGAQGDLTTECATVNSPTAIMSIEYFDEDFDLKDQDI

Parental  GRPKELTIRTQKFKATLWMCEEFPLSLVEQVIPIIDLMARTSAHFARLRDFIKLDFPPGFPVKIEIPL-F
          GRPKELTIRTQKFKATLWMCEEFPLSLVEQVIPIIDLMART.AHFARLRDFIKLDFPPGFPVKIEIPL.F
Retrocopy GRPKELTIRTQKFKATLWMCEEFPLSLVEQVIPIIDLMARTRAHFARLRDFIKLDFPPGFPVKIEIPL>F

Parental  HVLNARITFGNVNGCSTAEERQSVEGTQAECAASDATNFEVDQSVFEIPESYHVQDNGRNVHLQDEDYEI
          HVLNARI.FGNVN.CSTAEERQSVEGTQAECAASDAT.FEVDQSVFEIP..YHVQDNGRNVHLQDEDYEI
Retrocopy HVLNARIMFGNVNDCSTAEERQSVEGTQAECAASDATDFEVDQSVFEIPAFYHVQDNGRNVHLQDEDYEI

Parental  MQFAIQQSLLESSRSQDLSGPASNGGVSHAHSYEAQYERAIQESLLTNMEGRCPGGLSDSSRFDSDL
          MQF.IQQSLLESSRS.DL.GPASNGG.S.AHSYEAQYERAIQESLLTNMEGRCPGGLS.SSRFDSDL
Retrocopy MQFTIQQSLLESSRS*DLLGPASNGGISYAHSYEAQYERAIQESLLTNMEGRCPGGLSESSRFDSDL

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	47.52 RPM
SRP017611_kidney	0.00 RPM	133.63 RPM
SRP017611_liver	0.00 RPM	36.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_986 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_986 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
Otolemur garnettii	ENSOGAG00000012287	1 retrocopy	retro_ogar_2792,
Rattus norvegicus	ENSRNOG00000001204	1 retrocopy	retro_rnor_986 ,
Rattus norvegicus	ENSRNOG00000011340	2 retrocopies	retro_rnor_2098, retro_rnor_2173,