RetrogeneDB ID: retro_itri_1797

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393805.1:174950..176330(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNMT3B
• Ensembl ID: ENSSTOG00000006657
• Aliases: None
• Description: DNA (cytosine-5-)-methyltransferase 3 beta [Source:HGNC Symbol;Acc:2979]

Sequence

>retro_itri_1797
GAGAACAAGAGTCGAAGACGCACAGTTGATGATTCAGCCGCCTCTGACCACTGTCCCCCAAACAAACGCCTCAAGACAAA
CTGCTATAACAATGGCAAGGACCGGGGAGAGGAAGATCAGAGCCGAGAACAAATGGTTTCTGATGTTACCAACAACAAGA
ACAATCTGGAAGATAGCTGTTTGTCCTGTGGTAGGAAAAACCCAGTGTCCTTCCACCCGCTCTTTGAGGGTGGGCTTTGC
CAGACATGCCAGGATCGCTTCTTTGAGCTCTTCTACATGTACCACGATGATGGTTACCAATCCTACTGTACCGTGTGCTG
TGGGGGCCATGAGCTGCTTCTCTGCAGCAATGCAAGCTGTTGCCGATGCTTCTGTGTGGAGTGTCTGGAGGTGCTGGTGG
GCAAGGGCACAGCGGAGGATGCCAAGCTGCAGGAGCCCTGGAGCTGCTACATGTGTCTCCCCCAGCGCTGCCACGGAGTC
CTGCGGGGCCAGAAGGACTGGAATGTCCGCCTGCAGACCTTCTTCACCAGCGACATGGGGCTCAAATACAAGGCCCCCAA
GTTGTACTCTGCGATTCCCGCAGCCAAAAGGCGGCCCATTTGAGTCCTGTCACTATTCGATGGGATTGCCACAGGTTACT
TGGTCCTCAAAGACTTGGGCATTAAAGTGGAAAAGTATGTTGCCTCGGAAGTGTGCGAAGAATCCATCGCTGTTGGAACC
GTGAAGCACGAGGGCAACATCAAATATATGAATGACGTTAGGAACATCACAAAGAAAAATATTGAAGAGTGGGGTCCATT
TGATTTGGTGATCGGTGGAAGCCCATGCAATGACCTATCAAATGTGAATCCTGCCCGGAAAGGCCTGTATGAGGGCACTG
GCCGACTCTTCTTCGAATTCTACCACCTGCTCAATTACTCACGCCCCAAAGAAGGGGATGACCAGCCGTTCTTCTGGATG
TTTGAGAATGTTGTAGCCATGAAGGTCGACGACAAGAGGGACATGTCATGGTTCCTGGAGTGCAACCCAGTGATGATTGA
TGCTATCAAAATTTCTGCTGCTCACAGGGCTCCATACTTCTGGGGAAACCTACCTGGGATGAACAGGCCTGTGATAGCAT
CAAAGAATGATAAGCTCCAGCTGCAGGACTGCTTGGAATTCAGTAGGACTGCAAAGTTAAAGAAAGTGCAGACAATAACC
ACCAAGTCCAACTCCATCAAACAGGGGGAAAACCAACTTTTCCCTGTTGTCATGAATGGCAAAGAAGATGTTTTGTGGTG
CACTGAGCTCGAAAGGATCTTCGGTTTTCCTGTGCACTACACGGATATGTCCAACATGGGCCACGGTGCCCGCCAGAAGC
TGCTTGGGCGGTCCTGGAGT

Alignment

ORF - retro_itri_1797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENKSRRRTVDDSAASDHCPPNKRLKTNCYNNGKDRGEEDQSREQMVSDVANNKNNLEDSCLSCGRKNPVS
          ENKSRRRTVDDSAASDHCPPNKRLKTNCYNNGKDRGEEDQSREQMVSDV.NNKNNLEDSCLSCGRKNPVS
Retrocopy ENKSRRRTVDDSAASDHCPPNKRLKTNCYNNGKDRGEEDQSREQMVSDVTNNKNNLEDSCLSCGRKNPVS

Parental  FHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGKGTAED
          FHPLFEGGLCQTC.DRF.ELFYMY.DDGYQSYCTVCC.G.ELLLCSN.SCCRCFCVECLEVLVGKGTAED
Retrocopy FHPLFEGGLCQTCQDRFFELFYMYHDDGYQSYCTVCCGGHELLLCSNASCCRCFCVECLEVLVGKGTAED

Parental  AKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQTFFTSDPGLEYEAPKLYPAIPAAKRRPIRVLSLFDGIA
          AKLQEPWSCYMCLPQRCHGVLR..KDWNVRLQTFFTSD.GL.Y.APKLY.AIPAAKRRPI.VLSLFDGIA
Retrocopy AKLQEPWSCYMCLPQRCHGVLRGQKDWNVRLQTFFTSDMGLKYKAPKLYSAIPAAKRRPI*VLSLFDGIA

Parental  TGYLVLKDLGIKVEKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLS
          TGYLVLKDLGIKVEKYVASEVCEESIAVGTVKHEGNIKY.NDVRNITKKNIEEWGPFDLVIGGSPCNDLS
Retrocopy TGYLVLKDLGIKVEKYVASEVCEESIAVGTVKHEGNIKYMNDVRNITKKNIEEWGPFDLVIGGSPCNDLS

Parental  NVNPARKGLYGTEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVDDKRDISRFLECNPVMIDA
          NVNPARKGLY..EGTGRLFFEFYHLLNYSRPKEGDD.PFFWMFENVVAMKVDDKRD.S.FLECNPVMIDA
Retrocopy NVNPARKGLY--EGTGRLFFEFYHLLNYSRPKEGDDQPFFWMFENVVAMKVDDKRDMSWFLECNPVMIDA

Parental  IKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEFSRTAKLKKVQTITTKSNSIKQGKNQLFPVVM
          IK.SAAHRA.YFWGNLPGMNRPVIASKNDKL.LQDCLEFSRTAKLKKVQTITTKSNSIKQG.NQLFPVVM
Retrocopy IKISAAHRAPYFWGNLPGMNRPVIASKNDKLQLQDCLEFSRTAKLKKVQTITTKSNSIKQGENQLFPVVM

Parental  NGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWS
          NGKEDVLWCTELERIFGFPVHYTD.SNMG.GARQKLLGRSWS
Retrocopy NGKEDVLWCTELERIFGFPVHYTDMSNMGHGARQKLLGRSWS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1797 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1797 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000006657	1 retrocopy	retro_itri_1797 ,