RetrogeneDB ID: retro_rnor_1124

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:84983038..84984616(+)
• Located in intron of: None

Retrocopy information

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

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_1124
ATGTCCAAGTCATTCCAGCAGTCTCTCGGTAGGGATTCACAGGGTCATGGGCGTGACCTGTCTGCAGCAGGAATAGGCCT
TCTTGCTGCTGCTACCCAGTCTTTAAGTATGCCAGCATCTCTTGGAAGGATGAACCAGGGTACTGCACGTCTTGCTAACT
TAATGAATCTTGGAATGAGTTCTTCATTGAATCAACAAGGAGCTCATAGTGCACTGTCTTCTGCTAGTACTTCTTCCCAT
AATTTGCAGTCTATATTTAACATTGGAAGTAGAGGTCCACTCCCTTTGTCTTCTCAACACCGTGGAGATACAGATCAGGC
CAGTAATATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTCGTTATCCAGAGGACAAGATTACTC
CTGAGAACTTGCCCCAAATTCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACATTGAGTTATGGTAGAGAT
GGCAGATCTGCTACACGGGAGCCACCATACAGAGTTCCTAGGGATGATTGGGAAGAAAAAAGGCATTTTAGAAGAGATAG
TTTTGATGATCGTGGTCCTAGTCTCAACCCAGTGCTTGATTATGACCATGGAAGTCGTTCTCAAGAATCTGGTTATTAGG
ACAGAATGGATTATGAAGATGACAGATTAAGAGATGGAGAAAGGTGTAGGGATGATTCTTTTTTTGGTGAGACCTCGCAT
AACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGACGTGGTCCTGGCCCCTTACAAGAGAGATCTCTCTTTGAGAA
AAAGAGGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTCCATGGACTCTTACCGAAGGGTTATCCCCATCTGTGCTCTA
TATGTGATTTGCCAGTTCATTCTAATAAGGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTT
CTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAATGGGTGATCCATTCATGCTGCAGCAGTC
AACAAACCCAGCACCGGGAATTCTGGGACCGCCACCTCCTTCATTTCATCTTGGAGGACCAGCAGTTGGACCAAGAGGAA
ATCTGGGTGCTGGTAATGGGAACCTACAGGGACCAAGACACATGCAAAAAGGCAGAGTGGAAACCAGCCGAGTTGTTCAC
ATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTATTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCA
TCTGATTCTAAATAAAATTAATGAGGCATTTATTGAAATGGCGACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATA
CAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAA
GGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGACGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTA
TTCTGACAGTGCTGTCCTCAAGCTTGCAGAGCCTTATGGGAAAATAAAAAATTATATA

Alignment

ORF - retro_rnor_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.43 %
• Parental protein coverage: 62.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAH
          MSKSFQQS.LGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLA.LMNLGMSSSLNQQGAH
Retrocopy MSKSFQQS-LGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLANLMNLGMSSSLNQQGAH

Parental  SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQ
          SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQ
Retrocopy SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQ

Parental  ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQE
          ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQE
Retrocopy ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQE

Parental  SGYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIED
          SGY.DRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIED
Retrocopy SGY*DRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIED

Parental  FHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTN
          FHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTN
Retrocopy FHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTN

Parental  PAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVE
          PAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVE
Retrocopy PAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVE

Parental  PFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQ
          PFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQ
Retrocopy PFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQ

Parental  KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI
          KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI
Retrocopy KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI

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	99.65 RPM
SRP017611_kidney	0.14 RPM	43.26 RPM
SRP017611_liver	0.07 RPM	14.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_rnor_1124 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB697339	84983907	84984216	99.4	307	1	304
CB698762	84983726	84984117	100	388	0	388

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1124 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,