RetrogeneDB ID: retro_rnor_2428

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:15755580..15756550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dmap1
• Ensembl ID: ENSRNOG00000019407
• Aliases: None
• Description: DNA methyltransferase 1-associated protein 1 [Source:RefSeq peptide;Acc:NP_001015006]

Sequence

>retro_rnor_2428
ATGGCTACGGGCACAGATGTACGAGACAGTCTAGAACTCGGGGATCCAGGAGATGCCGCTGCTGGGACGGACCATCGGCA
AAAAGGATATTATCAACTCGGACAAGAAAAGTGCAAGAAGTCCTCAGAGACTCTGACCTTCAAGAGGCTTGAGCATGCAT
CGGGAGGTCTATGCTTTCCTTTACTCTGACAAAAAGGATGCACCCCGACTACTTCCCAGTGACACTGGTCAGGACATCGA
AAAGTGAAAGCTAAATTGTGGTCCAAGAAGGTTCGATCTTGGAAGCAGATGCCATTTACCAACCCAGCTCAAAAGGATGG
TGCTATGTTTTTCCACTGGTGCGGAGCAGTAGTGGAGGGCAAGGACTACCCTTTCACCAGGTTCAATAAGACAGTGCAAG
TGCCAGTGTACTCAGAGCAGGAGTGCCAAGTCTACCTTCATGACGATGCATGGACTAAGACAGAGACTGACCATCTCTTT
GACCTCAGCCGCTGATTTGATCTGCGCTTCGTAGTTATTCACGATCGGTATGACCCCCCGCAGTTCAAGAAGCGTTCTGT
GGAGTACCTGAAAGAGAGGTACTACCACATTTGTGCCAGGCTTGCCAACGTGAAGGCTGTGCCAGGTACAGATCTCAAAA
TACCAGTATTTGAGGCTGGGCATGAGAGACGGTGGAAGGAATAGCTGGAGCGACTTTACAACCAAACCCCAGAGCAGGTG
GCAGAGGAGGAGTACCTGCTCCAGGAGCTCTGTAAGATTGAGACCCGGAAAAAATCATGAGAAGCACAGCCAAGATCTGC
AGAAGTTGATTTCTGCAGCAGACACCACTGCAGAGCAGCGGCGCACAGAATGCAAGGCTCCCAAGAAGAAGCCACCCCAA
AAGAAGGAAGCTGAGAAGCCGGGTGTTTCTGAGACTACAGGCATCAAGTTTCCAGATTTTAAATCAGCAGGTGTGACATT
ATGGAGCCAG

Alignment

ORF - retro_rnor_2428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.61 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATGADVRDILELGGPEGDAASG-TISKKDIINPDKKKSKKSSETLTFKRPEGMHREVYALLYSDKKDAP
          MATG.DVRD.LELG.P...AA...TI.KKDIIN.DKK.S..S...L...R...MHREVYA.LYSDKKDAP
Retrocopy MATGTDVRDSLELGDPGDAAAGT>TIGKKDIINSDKK-SARSPQRL*PSRGLSMHREVYAFLYSDKKDAP

Parental  PLLPSDTGQ-GYRTVKAKLGSKKVRPWKWMPFTNPARKDGAMFFHWRRAAEEGKDYPFARFNKTVQVPVY
          .LLPSDTGQ.G.R.VKAKL.SKKVR.WK.MPFTNPA.KDGAMFFHW..A..EGKDYPF.RFNKTVQVPVY
Retrocopy RLLPSDTGQ<GHRKVKAKLWSKKVRSWKQMPFTNPAQKDGAMFFHWCGAVVEGKDYPFTRFNKTVQVPVY

Parental  SEQEYQLYLHDDAWTKAETDHLFDLSRRFDLRFVVIHDRYDHQQYKKRSVEDLKERYYHICAKLANVRAV
          SEQE.Q.YLHDDAWTK.ETDHLFDLSR.FDLRFVVIHDRYD..Q.KKRSVE.LKERYYHICA.LANV.AV
Retrocopy SEQECQVYLHDDAWTKTETDHLFDLSR*FDLRFVVIHDRYDPPQFKKRSVEYLKERYYHICARLANVKAV

Parental  PGTDLKIPVFDAGHERRRKEQLERLYNRTPEQVAEEEYLLQELRKIEARKKEREKRSQDLQ-KLITAADT
          PGTDLKIPVF.AGHERR.KE.LERLYN.TPEQVAEEEYLLQEL.KIE.RKK..E............A..T
Retrocopy PGTDLKIPVFEAGHERRWKE*LERLYNQTPEQVAEEEYLLQELCKIETRKKS*EAQPRSAE>LISAADTT

Parental  TAEQRRTERKAPKKKLPQKKEAEKPAVPETAGIKFPDFKSAGVTLRSQ
          ....R.TE.KAPKKK.PQKKEAEKP.V.ET.GIKFPDFKSAGVTL.SQ
Retrocopy AEQRR-TECKAPKKKPPQKKEAEKPGVSETTGIKFPDFKSAGVTLWSQ

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	0.00 RPM	19.27 RPM
SRP017611_kidney	0.00 RPM	12.56 RPM
SRP017611_liver	0.00 RPM	8.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2428 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003922	1 retrocopy	retro_cjac_2754,
Mus musculus	ENSMUSG00000009640	1 retrocopy	retro_mmus_1744,
Rattus norvegicus	ENSRNOG00000019407	4 retrocopies	retro_rnor_2428 , retro_rnor_2504, retro_rnor_2507, retro_rnor_2940,