RetrogeneDB ID: retro_rnor_2940

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:74792465..74793870(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022251
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2940
ATGGCTACGGGCGCAGATGTATGAGACATTCTAGAACTCGGGGGTCCAGAGGGAGGTGCCCCTTCTGGGACCATCAGCAA
AAAGGATATTATCAACCCGGACAAGAAAAAGTCCAAGAAGCCCTCAGAGACACTGACCTTCAAGAGGCCGGAGAGCATGC
ATTGGGAGGTCTATGCTTTGCTTTACTCTGACAAAAGGGACGCACCCCCACTACTTCCCAGTGACACCGGTCAGGGGTAC
CGGACAGTGAAGGCTAAGTTGGGGTCCAAGAAGGTTCGACCTTGGAAGTGGATGCCATTTACCAACCCAGCTCGAAAGGA
TGGTGCTATGTTTTTCCACTGGCGCCGAGCAGCGGAGGAGGGCAAGGACTACCCCTTCGCCAGGTTCAATAAGACAGTGC
AGGTGCCAGTGTACTCAAAGCAGGAGGACCAGCTCTACCTTCATGATGGTGCATGGACTAAGGCAGAGGCTGACCATCTC
TTTGACCTCAGCCGCCGATTTGATCTGCGCTTCGTAGTTATTCACGATCGGTATGACCACCAGCAGTACAAGAAGCGTTC
TGTGGAGGACCTGAAAGAGAGGTACTACCACATTTGTGCCAAGCTTGCCAACGTGAGGGCTGTGCCAGGTACAGATCTCA
AAATACCAGTATTTGATGCCGGGCATGAGAGACGGCGGAAGGAACAGCTGGAGCGACTTTACAACCGAACCCCAGAGCAG
GTGGCAGAGGAGGAGTACCTGCTCCAGGAGCTTCGTAAGATTGAGGCCCGGAAAAACGAGCTGGAGAAGCGCAGCCAAGA
CCTGCAGAAGCTGATTACTGCAGCAGACACCACCGCAGAGCAGCGGCGCACAGAACGCAAGGCTCCCAAGAAGAAGCTAC
CCCAGAAGAAGGAGGCTGAGGAGCCGGCTGTTCCTGAGACTGCAGACATCAAGTTTCCAGATTTTAAGTCAGCAGGTGTG
ACATTATGGAGCCAGCGGATGAAGCTGCCCAGCTCTGTGGGTCAGAAGAAGATCAAGGCGCTGGAACAGATGCTGCTGGA
ACTTGGTGTGGAGCTGAGCCCTACCCCCACAGAGGAGCTGGTGCATATGTTCAATGAGTTGCGGAGTGACCTGGTGTTAC
TCTACGAGCTCAAGCGGGCCTGTGCCAACTGTGAATATGAGCTACAGATGCTACAGCACCGGCATGAGGCCCTGGCTCGG
GCAGGAGTGCTGGGGGGCCCTGCCACACCAGCAGTGGGACCAACCCCAGCGTCTGCTGAGCCAACAGTGTCTGAATCTGG
ACTTGGTCTTGACCCCTAGCAAGGACACCATTATTGATGTCGTGGGTGCACCGCTCACACCCAATTCGCGGAAACCACGG
GAATCAGCCTCCAGCTCATCTTCTGTGAAGAAAGCCAAGAAACCA

Alignment

ORF - retro_rnor_2940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATGADVRDILELGGPEGDAASGTISKKDIINPDKKKSKKSSETLTFKRPEGMHREVYALLYSDKKDAPP
          MATGADV.DILELGGPEG.A.SGTISKKDIINPDKKKSKK.SETLTFKRPE.MH.EVYALLYSDK.DAPP
Retrocopy MATGADV*DILELGGPEGGAPSGTISKKDIINPDKKKSKKPSETLTFKRPESMHWEVYALLYSDKRDAPP

Parental  LLPSDTGQGYRTVKAKLGSKKVRPWKWMPFTNPARKDGAMFFHWRRAAEEGKDYPFARFNKTVQVPVYSE
          LLPSDTGQGYRTVKAKLGSKKVRPWKWMPFTNPARKDGAMFFHWRRAAEEGKDYPFARFNKTVQVPVYS.
Retrocopy LLPSDTGQGYRTVKAKLGSKKVRPWKWMPFTNPARKDGAMFFHWRRAAEEGKDYPFARFNKTVQVPVYSK

Parental  QEYQLYLHDDAWTKAETDHLFDLSRRFDLRFVVIHDRYDHQQYKKRSVEDLKERYYHICAKLANVRAVPG
          QE.QLYLHD.AWTKAE.DHLFDLSRRFDLRFVVIHDRYDHQQYKKRSVEDLKERYYHICAKLANVRAVPG
Retrocopy QEDQLYLHDGAWTKAEADHLFDLSRRFDLRFVVIHDRYDHQQYKKRSVEDLKERYYHICAKLANVRAVPG

Parental  TDLKIPVFDAGHERRRKEQLERLYNRTPEQVAEEEYLLQELRKIEARKKEREKRSQDLQKLITAADTTAE
          TDLKIPVFDAGHERRRKEQLERLYNRTPEQVAEEEYLLQELRKIEARK.E.EKRSQDLQKLITAADTTAE
Retrocopy TDLKIPVFDAGHERRRKEQLERLYNRTPEQVAEEEYLLQELRKIEARKNELEKRSQDLQKLITAADTTAE

Parental  QRRTERKAPKKKLPQKKEAEKPAVPETAGIKFPDFKSAGVTLRSQRMKLPSSVGQKKIKALEQMLLELGV
          QRRTERKAPKKKLPQKKEAE.PAVPETA.IKFPDFKSAGVTL.SQRMKLPSSVGQKKIKALEQMLLELGV
Retrocopy QRRTERKAPKKKLPQKKEAEEPAVPETADIKFPDFKSAGVTLWSQRMKLPSSVGQKKIKALEQMLLELGV

Parental  ELSPTPTEELVHMFNELRSDLVLLYELKQACANCEYELQMLRHRHEALARAGVLGGPATPAVGPTPASAE
          ELSPTPTEELVHMFNELRSDLVLLYELK.ACANCEYELQML.HRHEALARAGVLGGPATPAVGPTPASAE
Retrocopy ELSPTPTEELVHMFNELRSDLVLLYELKRACANCEYELQMLQHRHEALARAGVLGGPATPAVGPTPASAE

Parental  PTVSESGLGLD-PSKDTIIDVVGAPLTPNSRKRRESASSSSSVKKAKKP
          PTVSESGLGLD.PSKDTIIDVVGAPLTPNSRK.RESASSSSSVKKAKKP
Retrocopy PTVSESGLGLD>PSKDTIIDVVGAPLTPNSRKPRESASSSSSVKKAKKP

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_2940 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2940 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 ,