RetrogeneDB ID: retro_rnor_1570

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:214981225..214983352(+)
• Located in intron of: ENSRNOG00000042221

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_1570
ATACCTAATCAGGGAGAAGACTGCTATTTTTATTTCTATTCTACATGCACCAAGGGTGACAGCTGCCCATTCCGTCACTG
TGAAGCTGCACTAGGAAATGAAACTGTTTGCACACTGTGGCAGGAAGGTCATTGTTTTCGACAGGTGTGCAAATTTCGCC
ACATGGAAATTGACAAAAAACGAAGTGAAATTCCTTGTTATTGGGAAAACCAGCCAATGGGATGTCAAAAATTAAATTGC
ACTTTCCATCACAACAGAAGTCGTTATGTCGATGGACTGTTCCTACTTCCAAGCAAAACTGTGTTACCCACTGTGCCTGA
GTCACAAGAAGAGGAAGTAAAGACCGGCCAGCTCACGGTTCAACAGAACAAATTGTCTGTTCAGTCCAACCCCTCCCCTC
AGCTGCGGAGCGTGATGAAAGTGGAGAGTTCGGAAAACGTTCCCAGCCCCACATACCCTCCTGTCGTGATCAATGCTGCC
GATGATGATGAAGATGACAATGTTTTCTGAGGAGGGTGATGAGAGCAAAACACCTGCCCTGCAGCCAACAACTGACGCCC
ATAATGGACTACAAGTGGCCTCTACCCGCAAACCTGGAGCCAGTTTAAAGCCAGGTGACTCTTTGAATTTTGGAATAAAA
ACGCTTGAGGAAATTAAATCAAAGAAAATGAAGGAAAAATCCAAGAAGCAAGGTGAAGGCTCCTCGGGAATTTCCAGTGT
TTTACATCAGCCTTAGCCCAATCCAGGCCCTGAGGAGAATGTTCGGACTGTGGTGAGAACCGTAACTCTGTCAAGCAAAC
AAGAAGAGCCCTTGGTTAGACTGAGTCTTACTGAGAGACTGGGGAAACGAAAACTTCCAGGAGATGGTGACAGTGATCCC
CCATTAAAGCGAAGTCTTGCACAGAGACTGGGAAAAAAAAGTGGAAGCACCAGAAACTAACATTGATAAAGCACCAAAGA
AAGAGAGAGTTAATAAAACTGGTGAGATCCATGTTAAGACACTGGAAGAAATTCTTCTTGAAAGAGCCAGTCAGAAACGT
GGAGAATTGCAAACTAAACTAAAGACAGAAGAACCTTCAGGAGCTGAGGATTCTCCATCAGGAACAAAAAGTTCTTCAGT
GCGCATCAAAACCTTCTCTGAGGTCCTGGCTGAAAAGAAACATCGGCAGCAGGAAATGGAAAGACAGAAATCCAAAAAGG
ATACAAGTTGCCTCATGCTAACAGAAGATTCTGAAGTGAAAAAGACTGTGAGCCTGCCGACTGTTGCTGTTAGCAAAGGA
CAGCTTGAGGAGGAGCCTGCAGACAGAGCCAGGCCTATGCAGGAGGTGCATATTAAGACGCTAGAGGAAATTAAGCTGGA
AAAGGCCCTGAGGGTGCAGCAAAGCGCTGAGAGGAGTGGCAGCTCCCGGCCTCAAGCGGAGGCTGCCCCAGTGGCCAAGA
GGCTGCTGCGCATCACCAAGAGATCAGGTGCAAGAGAAGAGAAAAAACTTGAACTTGAGGACAGTGGTGGCGCTCCCTCT
CAGAGCAGTGTGACTAAGATGGGACTTAGTGAGACTTCAGATGAGACCATAAGTGATCCCACAAAACTTCCAGTCAACAG
ATGTGACATTGTCAAAGAGAAACACACACAGAGACAGCAAGAGAGAGGAGCATCACAAAAGGAGAAGCCAGCCTTGGCAT
CTGTGCGGACAGATGAGGCTTCTTACTATACCCGAGTGGTGGGGAAGCCGGTGCTCACTGCTGTATCGGGCGTCACTTGG
CACCTGGCAAAACGGCTCCCCACAGAGTCGTCCCAGAAAGGGGAGGTGGAGACCTCCGGGATTGGAGACTCAATACTGCA
CGTGAAGTGTGCGGCACAGACTCTGGAGAAAAGAGGTAAAGCCAAGCCCAAAGTAAATGTGAAGCCATCTGTGGTCAAGG
TTGTCTCAGCCCCCAAATTGGCTCCCAAGCGCAAGGCTGTGGAGGTGCACTCTGCTGTCATCGCAGCTGTGAAGCCGCTC
AGCTCCAGCAGTGTCCTGCAGGAAAGCCGCCAAGAAAGCAGCCGTGGCTGTTGTCCCACTCCTCTCTGAGGATAAATCCG
TCACTATGTCTGAGACAGAAAAACCGAAAGACAGTTCTGCGCTGTCT

Alignment

ORF - retro_rnor_1570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.21 %
• Parental protein coverage: 90.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWEN
          .PNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEG.CFRQVC.FRHMEIDKKRSEIPCYWEN
Retrocopy IPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGHCFRQVCKFRHMEIDKKRSEIPCYWEN

Parental  QPMGCQKLNCAFHHNRSRYVDGLFLPPSKTVLPTVPESQEEEVKTSQLMVQQNKLSVQSNPCPQLRSVMK
          QPMGCQKLNC.FHHNRSRYVDGLFL.PSKTVLPTVPESQEEEVKT.QL.VQQNKLSVQSNP.PQLRSVMK
Retrocopy QPMGCQKLNCTFHHNRSRYVDGLFLLPSKTVLPTVPESQEEEVKTGQLTVQQNKLSVQSNPSPQLRSVMK

Parental  VESSENVPSPTHPPVVINAADDDEDDDDQ-FSEEGDESKTPALQPTTDAHNGLRVASTRKPGASLKPGDS
          VESSENVPSPT.PPVVINAADDDE..DD..FSEEGDESKTPALQPTTDAHNGL.VASTRKPGASLKPGDS
Retrocopy VESSENVPSPTYPPVVINAADDDE--DDN>FSEEGDESKTPALQPTTDAHNGLQVASTRKPGASLKPGDS

Parental  LNFGIKTLEEIKSKKMKEKSKKQGEGSSGMSSVLHQPQPNPGPEKENVRTVVRTVTLSSKQEEPLVRLSL
          LNFGIKTLEEIKSKKMKEKSKKQGEGSSG.SSVLHQP.PNPGPE.ENVRTVVRTVTLSSKQEEPLVRLSL
Retrocopy LNFGIKTLEEIKSKKMKEKSKKQGEGSSGISSVLHQP*PNPGPE-ENVRTVVRTVTLSSKQEEPLVRLSL

Parental  TERLGKRKLPGGGDNDPPLKRSLAQRLGKK-VEAPETNIDKAPKKDEQERVNKTGEIHVKTLEEILLERA
          TERLGKRKLPG.GD.DPPLKRSLAQRL....VEAPETNIDKAPKK...ERVNKTGEIHVKTLEEILLERA
Retrocopy TERLGKRKLPGDGDSDPPLKRSLAQRLXXX>VEAPETNIDKAPKK---ERVNKTGEIHVKTLEEILLERA

Parental  NQKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSEV
          .QKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSEV
Retrocopy SQKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSEV

Parental  KKTVSLPTVAVSKGQLEEEPAGRARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRLL
          KKTVSLPTVAVSKGQLEEEPA.RARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRLL
Retrocopy KKTVSLPTVAVSKGQLEEEPADRARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRLL

Parental  RITKRSGTREEKKLELEDNGGAPSQSSVTKMGVSETSDETISDPTKLPVNRCDIVKEKHTQRQQERGASQ
          RITKRSG.REEKKLELED.GGAPSQSSVTKMG.SETSDETISDPTKLPVNRCDIVKEKHTQRQQERGASQ
Retrocopy RITKRSGAREEKKLELEDSGGAPSQSSVTKMGLSETSDETISDPTKLPVNRCDIVKEKHTQRQQERGASQ

Parental  KEKPALASVRTDEASYYTRVVGKPVLTAVSGVTRHLAKRLPTESSQKGEVETSGIGDSILHVKCAAQTLE
          KEKPALASVRTDEASYYTRVVGKPVLTAVSGVT.HLAKRLPTESSQKGEVETSGIGDSILHVKCAAQTLE
Retrocopy KEKPALASVRTDEASYYTRVVGKPVLTAVSGVTWHLAKRLPTESSQKGEVETSGIGDSILHVKCAAQTLE

Parental  KRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES-PAKK-AAVKVRKILGY
          KRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES.P..K.AAV.V...L..
Retrocopy KRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES<PPRK<AAVAVVPLLSE

Parental  PRSPTMPKDSSALSSAQAS
          ..S.TM........S...S
Retrocopy DKSVTMSETEKPKDSSALS

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	0.00 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_1570 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1570 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,