RetrogeneDB ID: retro_rnor_2504

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:15769068..15770035(-)
• 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_2504
ATGGCTACGAGCACAGAGGTACAAGACATTCTAGAACTCGGGGATCCAGGAGATGCCGCTTCTGGGACCATCGGCAAAAA
GGATATTATGAACCCGGACAAGAAAAGTGCAAGAAGTCCTCAGAGGCTCTGACCTTCAAGAGGCTTGAGCATGCATCGGG
AGGTCTATGCTTTCCTTTACTCTGACAAAAAGGATGCACCCCGACTATTTCCCAGTGACACTGGTCAGGAGTATCGAGCA
GTGAAGGCTAAATTGGGGTCCAAGAAGGTTCGATCTTGGAAGTGGATGCCATTTACCAACCCAGGTTGAAAGGATGGTGC
TATGTTTTTCCACTGGTGCCGAGCAGTAGTGGAGGGCAAGGACTACCCTTTCGCCAGGTTCAATAAGACAGTGCAAGTGC
CAGTGTACTCAGAGCAGGAGTACCAAATCTACCTTCATGACGATGCATGGACTAAGGCAGAGACTGACCATCTCTTTGAC
CTCAGCCACCGATTTGATCTGCGCTTCGTAGTTATTCACGATCGGCATGACCACCAGCAGTTCAAGAAGCGTTCTGTGGA
GGACCTGAAAGAGAGGTACTACCACATTTGTGCCAGGCTTGCCAACGTGAAGGCTGTGCCAGGTACAGATCTCAAAATAC
CAGTATTTGAGGCTGGGCATGAGAGACGGCGGAAGAAATAGCTGGAGCGACTTTACAACCGAACCCCAGAGCAGGTGGCA
AAGGAGGAGTACCTGCTACAGGAGCTTCGTAAGATTGAGACCTGGAATAAATCAGGAGAAGCACAGCCAAGACCTGCAGA
AGTTGATTTCTGCAGCGGACACCACTACGGAGCGGCAGCACATAGAATGCAAGGCTCCCAAGAAGAAGCTGCCCCAGAAG
AAGGAGGCTGAGAAGCCGGGTGTTTCTGAGACTACAGGCATCAAGTTTCCAGATTTTAAGTCAGCAGGTTTGACATTATG
AAGCCAG

Alignment

ORF - retro_rnor_2504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATGADVRDILELGGPEGDAASGTISKKDIINPDKKKSKKSSETLTFKRPEGMHREVYALLYSDKKDAPP
          MAT...V.DILELG.P.GDAASGTI.KKDI.NPDKK.S..S...L...R...MHREVYA.LYSDKKDAP.
Retrocopy MATSTEVQDILELGDP-GDAASGTIGKKDIMNPDKK-SARSPQRL*PSRGLSMHREVYAFLYSDKKDAPR

Parental  LLPSDTGQGYRTVKAKLGSKKVRPWKWMPFTNPARKDGAMFFHWRRAAEEGKDYPFARFNKTVQVPVYSE
          L.PSDTGQ.YR.VKAKLGSKKVR.WKWMPFTNP..KDGAMFFHW.RA..EGKDYPFARFNKTVQVPVYSE
Retrocopy LFPSDTGQEYRAVKAKLGSKKVRSWKWMPFTNPG*KDGAMFFHWCRAVVEGKDYPFARFNKTVQVPVYSE

Parental  QEYQLYLHDDAWTKAETDHLFDLSRRFDLRFVVIHDRYDHQQYKKRSVEDLKERYYHICAKLANVRAVPG
          QEYQ.YLHDDAWTKAETDHLFDLS.RFDLRFVVIHDR.DHQQ.KKRSVEDLKERYYHICA.LANV.AVPG
Retrocopy QEYQIYLHDDAWTKAETDHLFDLSHRFDLRFVVIHDRHDHQQFKKRSVEDLKERYYHICARLANVKAVPG

Parental  TDLKIPVFDAGHERRRKEQLERLYNRTPEQVAEEEYLLQELRKIEARKKEREKRSQDLQ-KLITAADTTA
          TDLKIPVF.AGHERRRK..LERLYNRTPEQVA.EEYLLQELRKIE...K..E............A..TT.
Retrocopy TDLKIPVFEAGHERRRKK*LERLYNRTPEQVAKEEYLLQELRKIETWNKSGEAQPRPAE>LISAADTTT-

Parental  EQRRTERKAPKKKLPQKKEAEKPAVPETAGIKFPDFKSAGVTLRSQ
          E....E.KAPKKKLPQKKEAEKP.V.ET.GIKFPDFKSAG.TL.SQ
Retrocopy ERQHIECKAPKKKLPQKKEAEKPGVSETTGIKFPDFKSAGLTL*SQ

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_2504 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2504 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,