RetrogeneDB ID: retro_rnor_176

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:107826209..107827496(+)
• Located in intron of: ENSRNOG00000009281

Retrocopy information

• Ensembl ID: ENSRNOG00000009639
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Zrsr2
• Ensembl ID: ENSRNOG00000033176
• Aliases: Zrsr2, RGD1559763
• Description: Protein Zrsr2 [Source:UniProtKB/TrEMBL;Acc:D3ZHQ8]

Sequence

>retro_rnor_176
ATGGCATCACAGCAGACCGCGTTTCCTGAGAAACTCAGCAGAAAACAATACAAGGCTGCAATGAAGAAGGAGAAACGCAA
GAAACGTCGGCAGAAAATGGCTCGCTTGAGAGCTCTGGAAGCCCCACCAGAGGTGGAGGAGGAGGATGTTTCTGCCAATG
AAGAACTTGCAGAGAGATTACTGGAGATAGAGAGGCAAAAATTACATGAAGAGTGGCTGCTGAGGGAGGAGAAGGCACAA
GAAGAATTCAGAATAAAGAAGAAAAAGGAGGAGGCTGCTAGAAAACAGAAGGAAGAACAGGAGAGACAAATAAAGGCTGA
ATGGGAAGAACAACAGAAAAAACAGAGAGAGGAGGAGGAGCAGAAGCTACAGGAGAAGAAAGAGAGAGAGGAAGCGGTGC
AGAAAATGCTGGACCAGGCTGAAAATGAAGGCACTTGGCAGAACCCAGAACCACCCAAAGATTTAAGGCTGGAGAAATAT
CGACCCAGTTGTCCCTTCTACAATAAGACGGGAGCCTGCAGATTTGGTAACAGGTGTTCACGGAAGCATGACTTTCCCAC
GTCAAGTCCCACACTTCTTGTGAAGAGTATGTTTACGACGTTTGGAATGGAGCAGTGCAGAAGGGATGACTACGACTCTG
ACGCAAACCTGGAGTACAGTGAGGAGGAGACCTACCAGCAGTTTTTGGATTTCTACCACGACGTGCTGCCCGAGTTCAAG
AACGTGGGAAAGGTGATTCAGTTCAAAGTAAGCTGCAATCTGGAACCTCATTTGCGGGGCAATGTGTATGTTCAGTACCA
GTCGGAAGAGGAATGCCAAGCAGCCCTCTCTCTCTTTAATGGAAGATGGTACGCAGGACGACAGCTGCAGTGTGAATTCT
GTCCAGTGACCCGGTGGAAGGTTGCGATTTGCGGTTTGTTCGAAATGCAAAAGTGTCCGAAAGGAAAGCACTGCAACTTC
CTCCATGTGTTCAGAAACCCCAACAACGAGTTCAGAGACGCGAACAGGGACATCTACCTGCCTCCGGCGAGCACTGGCTC
CTCTGGTAAAAACTCAGACCGGGGGGACAGGAAGGATCACCGAGAGGAAAGCTACAGCAAGTCAAGAAGCCACCACTCTG
GCTCATACCACTCCTCCAAGAGAAGCAGGGAGTCGGAGAGGAAGAGTCCTCACAGGTGGAAGAAATCTCACAAACAGGCC
ACGAAGAGTCATGAGCGGCACAGCTCAAGAAGAGGAAGAGAAGAGGGCAGCAGTCCAGGTCCGCAAAGCCAGAGCCACAG
AACCTGA

Alignment

ORF - retro_rnor_176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 81.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRKKYMALRKKEKRKKRRQELARLRDAELSQKEEEEDPLGEEKRLEEERLLEAERQRLHEEWLLREEKAQ
          SRK.Y.A..KKEKRKKRRQ..ARLR..E.....EEED....E...E..RLLE.ERQ.LHEEWLLREEKAQ
Retrocopy SRKQYKAAMKKEKRKKRRQKMARLRALEAPPEVEEEDVSANEELAE--RLLEIERQKLHEEWLLREEKAQ

Parental  EEFRAKKRKEEAARKRKEELERKLKAEWEEQQRKEREEEEQKQQEKREREEAAQKRLDQAENELENGGTW
          EEFR.KK.KEEAARK.KEE.ER..KAEWEEQQ.K.REEEEQK.QEK.EREEA.QK.LDQAENE....GTW
Retrocopy EEFRIKKKKEEAARKQKEEQERQIKAEWEEQQKKQREEEEQKLQEKKEREEAVQKMLDQAENE----GTW

Parental  QNPEPPTDIRVLEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFGMEQCRRDDYDPDS
          QNPEPP.D.R.LEK.R..CPFY.KTGACRFG.RCSRKH.FPTSSPTLL.KSMFTTFGMEQCRRDDYD.D.
Retrocopy QNPEPPKDLR-LEKYRPSCPFYNKTGACRFGNRCSRKHDFPTSSPTLLVKSMFTTFGMEQCRRDDYDSDA

Parental  SLEYSEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYA
          .LEYSEEETYQQFLDFY.DVLPEFK.VGKVIQFKVSCNLEPHLRGNVYVQYQSEE.CQAA.S.FNGRWYA
Retrocopy NLEYSEEETYQQFLDFYHDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEECQAALSLFNGRWYA

Parental  GRQLQCEFCPVTRWKMAICGLFEVQQCPRGKHCNFLHVFRNPNNEYREANRDIYLSPDWTSSSFAKSSER
          GRQLQCEFCPVTRWK.AICGLFE.Q.CP.GKHCNFLHVFRNPNNE.R.ANRDIYL.P..T.SS..K.S.R
Retrocopy GRQLQCEFCPVTRWKVAICGLFEMQKCPKGKHCNFLHVFRNPNNEFRDANRDIYLPPASTGSS-GKNSDR

Parental  RERASHYDEYYGRSRRRRSPSPGLSYKRNGESDRKSSSNHRVKKSHKHGMKNRERHSSRSRRRKRDHSLG
          ..R..H..E.Y..SR...S.S...S.KR..ES.RKS...HR.KKSHK...K..ERHSSR.R.R....S.G
Retrocopy GDRKDHREESYSKSRSHHSGSYH-SSKRSRESERKSP--HRWKKSHKQATKSHERHSSR-RGREEGSSPG

Parental  PWSQSRRS
          P.SQS.R.
Retrocopy PQSQSHRT

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	24.30 RPM	27.90 RPM
SRP017611_kidney	7.54 RPM	9.42 RPM
SRP017611_liver	6.52 RPM	6.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_176 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_176 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_233

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009333	1 retrocopy	retro_fcat_44,
Homo sapiens	ENSG00000169249	1 retrocopy	retro_hsap_39,
Gorilla gorilla	ENSGGOG00000011962	1 retrocopy	retro_ggor_1422,
Macaca mulatta	ENSMMUG00000014054	1 retrocopy	retro_mmul_2030,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233,
Nomascus leucogenys	ENSNLEG00000009496	1 retrocopy	retro_nleu_1,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25,
Rattus norvegicus	ENSRNOG00000033176	1 retrocopy	retro_rnor_176 ,
Tarsius syrichta	ENSTSYG00000005278	1 retrocopy	retro_tsyr_1826,