RetrogeneDB ID: retro_rnor_475

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:126981967..126984499(+)
• Located in intron of: ENSRNOG00000023496

Retrocopy information

• Ensembl ID: ENSRNOG00000016498
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Matr3
• Ensembl ID: ENSRNOG00000019875
• Aliases: Matr3, P130/MAT3
• Description: Matrin-3 [Source:UniProtKB/Swiss-Prot;Acc:P43244]

Sequence

>retro_rnor_475
ATGTCCAAGTCATTCCAGCAGTCATCTCTCGGTAGGGATTCACAGGGTCATGGGCGTGACCTGTCTGCAGCAGGAATAGG
CCTTCTTGCTGCTGCTACCCAGTCTTTAAGTATGCCAGCATCTCTTGGAAGGATGAACCAGGGTACTGCACGCCTTGCTA
GCTTAATGAATCTTGGAATGAGTTCTTCATTGAATCAACAAGGAGCTCATAGTGCACTGTCTTCTGCTAGTACTTCTTCC
CATAATTTGCAGTCTATATTTAACATTGGAAGTAGAGGTCCACTCCCTTTGTCTTCTCAACACCGTGGAGATACAGACCA
GGCCAGTAATATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTCGTTATCCAGAGGACAAGATTA
CTCCTGAGAACTTGCCCCAAATTCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACATTGAGTTATGGTAGA
GATGGCAGATCTGCTACACGGGAGCCACCATACAGAGTACCTAGGGATGATTGGGAAGAAAAAAGGCATTTTAGAAGAGA
TAGTTTTGATGATCGTGGTCCTAGTCTCAACCCAGTGCTTGATTATGACCATGGAAGTCGTTCTCAAGAATCTGATTATT
ATGACAGAATGGATTATGAAGATGACAGATTAAGAGATGGAGAAAGGTGTAGGGATGATTCTTTTTTTGGTGAGACCTCG
CATAACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGACGTGGTCCTGGCCCCTTACAAGAGAGATCTCTCTTTGA
GAAAAAGAGGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTCCATGGACTCTTACCGAAGGGTTATCCCCATCTGTGCT
CTATATGTGATTTGCCAGTTCATTCTAATAAAGGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCA
GCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAATGGGTGATCCATTCATGCTGCAGC
AGTCAACAAACCCAGCACCGGGAATTCTGGGACCGCCACCTCCTTCATTTCATCTTGGAGGACCAGCAGTTGGACCAAGA
GGAAATCTGGGTGCTGGTAATGGGAACCTACAGGGACCAAGACACATGCAAAAAGGCAGAGTGGAAACCAGCCGAGTTGT
TCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTATTACAACTGGTAGAACCATTTGGAGTCATTTCAA
ATCATCTGTTTCTAAATAAAATCAATGAGGCATTTATTGAAATGGCGACCACAGAAGATGCTCAGGCTGCTGTGGATTAT
TATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACC
TGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGACGTGTGATACATCTCAGCAATTTACCTCATTCTG
GCTATGCTGACAGTGCTGTCCTCAAGCTTGCAGAGCCTTATGGGAAAATAAAAAATTATATATTGATGAGGATGAAAAGT
CAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTCTAAAGAAGGCACTTTGGTTTCA
GGGAAGATGTGTTAAAGTTGACTTGTCTGAGAAATATAAAAAACTGGTGCTGAGGATTCCTAACAGAGGCATTGACTTAC
TGAAAAAAGATAAATCTCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGAT
GGTGCTCAGAAGACTGAGAATCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAAGACACCAA
GGATGACCAGACAGAACAGGAGCCCAGTATACTTCTTGAATCTGAAGATGAATTGCTTGTCGATGAGGAAGAAGCTGCAG
CACTACTAGAAAGTGGAAGCTCAGTGGGTGATGAGACTGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAG
GAGCCTTCAGATAAAGCTGTGAAAAAAGATGCAAGTGCAACATCCAAGAAAAAACTTAAAAAGGTGGACAAGATTGAGGA
ACTTGATAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCAGGTGCTGAATCTGCTGA
GAATGCTGATGATCCAAACAAAGACGCAAGTGATAATTCAGATGGCCAAAATGATGAGAACAAGGAGGACTATACAATTC
CAGATGAGTATAGAATTGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTAC
TGTAAGCTGTGTTCACTCTTTTATACAAATGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATT
AAAGAAATTTCTGAATAAATTGGCAGAAGAACGGAGGCAGAAGAAGGAAACT

Alignment

ORF - retro_rnor_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAH
          MSKSFQQSSLGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAH
Retrocopy MSKSFQQSSLGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAH

Parental  SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQ
          SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQ
Retrocopy SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQ

Parental  ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQE
          ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQE
Retrocopy ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQE

Parental  SGYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIED
          S.YYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIED
Retrocopy SDYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIED

Parental  FHGLLPKGYPHLCSICDLPVHSNK-EWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQST
          FHGLLPKGYPHLCSICDLPVHSNK.EWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQST
Retrocopy FHGLLPKGYPHLCSICDLPVHSNK>EWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQST

Parental  NPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLV
          NPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLV
Retrocopy NPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLV

Parental  EPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFD
          EPFGVISNHL.LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFD
Retrocopy EPFGVISNHLFLNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFD

Parental  QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF
          QKQELGRVIHLSNLPHSGY.DSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF
Retrocopy QKQELGRVIHLSNLPHSGYADSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF

Parental  QGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGAQKTENPAEGKEQEE
          QGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGAQKTENPAEGKEQEE
Retrocopy QGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGAQKTENPAEGKEQEE

Parental  KSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKA
          KSGEDGEKDTKDDQTEQEPS.LLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKA
Retrocopy KSGEDGEKDTKDDQTEQEPSILLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKA

Parental  VKKDASATSKKKLKKVDKIEELDQ-ENEAALENGIKNEENTEPGAESAENADDPNKDASDNSDGQNDENK
          VKKDASATSKKKLKKVDKIEELD..ENEAALENGIKNEENTEPGAESAENADDPNKDASDNSDGQNDENK
Retrocopy VKKDASATSKKKLKKVDKIEELDK<ENEAALENGIKNEENTEPGAESAENADDPNKDASDNSDGQNDENK

Parental  EDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEE
          EDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTN.EVAKNTHCSSLPHYQKLKKFLNKLAEE
Retrocopy EDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTN-EVAKNTHCSSLPHYQKLKKFLNKLAEE

Parental  RRQKKET
          RRQKKET
Retrocopy RRQKKET

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	0.50 RPM	99.65 RPM
SRP017611_kidney	0.00 RPM	43.26 RPM
SRP017611_liver	0.00 RPM	14.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_475 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_475 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475 ,