RetrogeneDB ID: retro_rnor_602

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:124318920..124321047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zc3h11a
• Ensembl ID: ENSRNOG00000002993
• Aliases: Zc3h11a, RGD1308290
• Description: zinc finger CCCH domain-containing protein 11A [Source:RefSeq peptide;Acc:NP_001041367]

Sequence

>retro_rnor_602
ATGCCTAATCAGGGAGAAGACTGCTATTTTTATTTCTATTCTACATGCACCAAAGGTGACAGCTGCCCATTCCGTCACTG
TGAAGCTGCACTAGGAAATGAAATTGTTTGCACACTATGGCAGGAAGGTCATTGTTTTCGACAGGTGTGCAATTTCGCCA
CATGGAAATTGACAAAAAACGAAGTGAAATTCCTTGTTATTGGGAAAACCAGCCAATGGGATGTCAAAAATTAAATTGCA
CTTTCCATCACAACAGAAGTCGTTATGTCGATGGACTGTTCCTACTTCCAAGCAAAACTGTGTTACCCACTGTGCCTGAG
TCACAAGAAGAGGAAGTAAAGACCGGCCAGCTCACGGTTCAACAGAACAAATTGTCTGTTCAGTCCAACCCCTCCCCTCA
GCTGCGGAGCGTGATGAAAGTGGAGAGTTCGGAAAACGTTCCCAGCCCCACATACCCTCCTGTCGTGATCAATGCTGCCG
ATGATGATGAAGATGACAATGTTTTCTGAGGAGGGTGATGAGAGCAAAACACCTGCCCTGCAGCCAACAACTGACGCCCA
TAATGGACTACAAGTGGCCTCTACCCGCAAACCTGGAGCCAGTTTAAAGCCAGGTGACTCTTTGAATTTTGGAATAAAAA
CGCTTGAGGAAATTAAATCAAAGAAAATGAAGGAAAAATCCAAGAAGCAAGGTGAAGGCTCCTCGGGAATTTCCAGTGTT
TTACATCAGCCTTAGCCCAATCCAGGCCCTGAGGAGAATGTTCGGACTGTGGTGAGAACCGTAACTCTGTCAAGCAAACA
AGAAGAGCCCTTGGTTAGACTGAGTCTTACTGAGAGACTGGGGAAACGAAAACTTCCAGGAGATGGTGACAGTGATCCCC
CATTAAAGCGAAGTCTTGCACAGAGACTGGGGAAAAAAAGTGGAAGCACCAGAAACTAACATTGATAAAGCACCAAAGAA
AGAGAGAGTTAATAAAACTGGTGAGATCCATGTTAAGACACTGGAAGAAATTCTTCTTGAAAGAGCCAGTCAGAAACGTG
GAGAATTGCAAACTAAACTAAAGACAGAAGAACCTTCAGGAGCTGAGGATTCTCCATCAGGAACAAAAAGTTCTTCAGTG
CGCATCAAAACCTTCTCTGAGGTCCTGGCTGAAAAGAAACATCGGCAGCAGGAAATGGAAAGACAGAAATCCAAAAAGGA
TACAAGTTGCCTCATGCTAACAGAAGATTCTGAAGTGAAAAAGACTGTGAGCCTGCCGACTGTTGCTGTTAGCAAAGGAC
AGCTTGAGGAGGAGCCTGCAGACAGAGCCAGGCCTATGCAGGAGGTGCATATTAAGACGCTAGAGGAAATTAAGCTAGAA
AAGGCCATGAGGGTGCAGCAAAGCGCTGAGAGGAGTGGCAGCTCCCGGCCTCAAGCGGAGGCTGCCCCAGTGGCCAAGAG
GCTGCTGCGCATCACCAAGAGATCAGGTGCAAGAGAAGAGAAAAAACTTGAACTTGAGGACAGTGGTGGCGCTCCCTCTC
AGAGCAGTGTGACTAAGATGGGAGTTAGTGAGACTTCAGATGAGACCATAAGTGATCCCACAAAACTTCCAGTCAACAGA
TGTGAACATTGTCAAAGAGAAACACACACAGAGACAGCAGGAGAGAGGAGCGTCACAAAAGGAGAAGCCAGCCTTGGCAT
CTGTGCGGACAGATGAGGCTTCTTACTATACCCGAATGGTGGGGAAGCCGGTGCTCACTGCTGTATTGGGCGTCACTTGG
CACCTGGCAAAACGGCTCCCCACGGAGTCGTCCCAGAAAGGGGAGGTGGAGACCTCCGGGATTGGAGACTCAATACTGCA
CGTGAAGTGTGCGGCACAGACTCTGGAGAAAAGGGGTAAAGCCAAGCCCAAAGTAAATGTGAAGCCATCTGTGGTCAAGG
TTGTCTCAGCCCCCAAATTGGCTCCCAAGCGCAAGGCTGTGGAGGTGCACTCTGCTGTCATCGCAGCTGTGAAGCCGCTC
AGCTCCAGCAGTGTCCTGCAGGAAAGCCGCCAAGAAAGCAGCCGTGGCTGTTGTCCCACTCCTCTCTGAGGATAAATCCG
TCACTATGTCTGAGACAGAAAAACCGAAAGACAGTTCTGCGCTGTCT

Alignment

ORF - retro_rnor_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 90.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFRQVC-RFRHMEIDKKRSEIPCYWE
          MPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNE.VCTLWQEG.CFRQVC..FRHMEIDKKRSEIPCYWE
Retrocopy MPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNEIVCTLWQEGHCFRQVC<QFRHMEIDKKRSEIPCYWE

Parental  NQPMGCQKLNCAFHHNRSRYVDGLFLPPSKTVLPTVPESQEEEVKTSQLMVQQNKLSVQSNPCPQLRSVM
          NQPMGCQKLNC.FHHNRSRYVDGLFL.PSKTVLPTVPESQEEEVKT.QL.VQQNKLSVQSNP.PQLRSVM
Retrocopy NQPMGCQKLNCTFHHNRSRYVDGLFLLPSKTVLPTVPESQEEEVKTGQLTVQQNKLSVQSNPSPQLRSVM

Parental  KVESSENVPSPTHPPVVINAADDDEDDDDQ-FSEEGDESKTPALQPTTDAHNGLRVASTRKPGASLKPGD
          KVESSENVPSPT.PPVVINAADDDE..DD..FSEEGDESKTPALQPTTDAHNGL.VASTRKPGASLKPGD
Retrocopy KVESSENVPSPTYPPVVINAADDDE--DDN>FSEEGDESKTPALQPTTDAHNGLQVASTRKPGASLKPGD

Parental  SLNFGIKTLEEIKSKKMKEKSKKQGEGSSGMSSVLHQPQPNPGPEKENVRTVVRTVTLSSKQEEPLVRLS
          SLNFGIKTLEEIKSKKMKEKSKKQGEGSSG.SSVLHQP.PNPGPE.ENVRTVVRTVTLSSKQEEPLVRLS
Retrocopy SLNFGIKTLEEIKSKKMKEKSKKQGEGSSGISSVLHQP*PNPGPE-ENVRTVVRTVTLSSKQEEPLVRLS

Parental  LTERLGKRKLPGGGDNDPPLKRSLAQRLGKK-VEAPETNIDKAPKKDEQERVNKTGEIHVKTLEEILLER
          LTERLGKRKLPG.GD.DPPLKRSLAQRLGKK.VEAPETNIDKAPKK...ERVNKTGEIHVKTLEEILLER
Retrocopy LTERLGKRKLPGDGDSDPPLKRSLAQRLGKK>VEAPETNIDKAPKK---ERVNKTGEIHVKTLEEILLER

Parental  ANQKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSE
          A.QKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSE
Retrocopy ASQKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSE

Parental  VKKTVSLPTVAVSKGQLEEEPAGRARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRL
          VKKTVSLPTVAVSKGQLEEEPA.RARPMQEVHIKTLEEIKLEKA.RVQQSAERSGSSRPQAEAAPVAKRL
Retrocopy VKKTVSLPTVAVSKGQLEEEPADRARPMQEVHIKTLEEIKLEKAMRVQQSAERSGSSRPQAEAAPVAKRL

Parental  LRITKRSGTREEKKLELEDNGGAPSQSSVTKMGVSETSDETISDPTKLPVNRCD-IVKEKHTQRQQERGA
          LRITKRSG.REEKKLELED.GGAPSQSSVTKMGVSETSDETISDPTKLPVNRC..IVKEKHTQRQQERGA
Retrocopy LRITKRSGAREEKKLELEDSGGAPSQSSVTKMGVSETSDETISDPTKLPVNRCE>IVKEKHTQRQQERGA

Parental  SQKEKPALASVRTDEASYYTRVVGKPVLTAVSGVTRHLAKRLPTESSQKGEVETSGIGDSILHVKCAAQT
          SQKEKPALASVRTDEASYYTR.VGKPVLTAV.GVT.HLAKRLPTESSQKGEVETSGIGDSILHVKCAAQT
Retrocopy SQKEKPALASVRTDEASYYTRMVGKPVLTAVLGVTWHLAKRLPTESSQKGEVETSGIGDSILHVKCAAQT

Parental  LEKRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES-PAKK-AAVKVRKIL
          LEKRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES.P..K.AAV.V...L
Retrocopy LEKRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES<PPRK<AAVAVVPLL

Parental  GYPRSPTMPKDSSALSSAQAS
          ....S.TM........S...S
Retrocopy SEDKSVTMSETEKPKDSSALS

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	0.07 RPM	48.89 RPM
SRP017611_kidney	0.07 RPM	52.69 RPM
SRP017611_liver	0.13 RPM	47.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_602 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_602 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000058673	2 retrocopies	retro_hsap_3481, retro_hsap_508,
Monodelphis domestica	ENSMODG00000001184	1 retrocopy	retro_mdom_1449,
Mus musculus	ENSMUSG00000026464	2 retrocopies	retro_mmus_3323, retro_mmus_564,
Otolemur garnettii	ENSOGAG00000000243	1 retrocopy	retro_ogar_3250,
Pan troglodytes	ENSPTRG00000001876	5 retrocopies	retro_ptro_2980, retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus	ENSRNOG00000002993	3 retrocopies	retro_rnor_1570, retro_rnor_1673, retro_rnor_602 ,