RetrogeneDB ID: retro_itri_1792

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393788.1:232366..233379(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MARK3
• Ensembl ID: ENSSTOG00000009776
• Aliases: None
• Description: MAP/microtubule affinity-regulating kinase 3 [Source:HGNC Symbol;Acc:6897]

Sequence

>retro_itri_1792
ATCATCATGAAGTATGCAAGTGGAGGTGAATTTTTGACTATATGATTCCACACAGAAGAATGAAGAAAAAAAGAAGCAAG
AGCTAAATTTAGACAAATCGTGTCTGCAGTACAGTATTGCCATCAAAAGCAATTGTTCACAGAGACCTCAAGGCAGAAAA
TCTGTTGTTAGATGCAGATATGAACATTAAAATAGCAGATTTTTGTTTTAGCAATGAGTTTACTTTGGTCACTAAACTAG
ATCCATTTTGTGGGAGTCCTCCATATGCAGCCCAAGAATTCTCCCAGAGCTAGAAGTACCATGAGCTGGACGTAGATGAG
TGGAGTCTTGGAATTATTCTGTACACTCTAGTCAACCAGTTGCTTTCCTCTGGGGGGATAGAATCTTGGAAGGAACTTAG
AGAGTTTTGAGGGAAATACAGAATCCTTTTCTACATATCCACAGGCTATGAAAAGCTGCTCAAATGCTTTCTGGTGCTAA
ACCCAATTAAGCTAGGCATTCCAGAGCAAATCACGAAGGACGGGTGGCTCAACGCAGGGCATGAGGAAGATGAACTTGAA
CCCTTTGTTGAACCAGAGCTGGACTAGAAGAGAATAGATATTATGGTAGGAGTGGGATATTCACAGGAAGAAATTCAAGA
ATCTCTCAGTAAAAGGAAATATGATGAAATCACAGCTACATAATTATTGTTGTGGAGAAAATCTGCAGAGCTGAACACTA
GTGACTCCAATTCTAACAGCAATTTTTCACTTGCTAAGGTGAGGCCAAGCAGTGACCTCAGCAACAGCACCAGACAGTCT
CCTCCCCACAAAGTGCAGAGAAGCTTTTCTTCAATCCAGAAGCAGAGAGCCTACAGTGATCATGCTGGACCAGCTATTCC
TTCAGTTGGGGCATATACCAAGAGGAGTCAGATAAGCATTGCTATTAGTGACCTCAAAGAAGATGGAATTCCCTCCAAGA
AATAAGGTTGCAGTGCAGTGGGAGGAGAGGCAGTTGCTCAAGCCAGTCCAATG

Alignment

ORF - retro_itri_1792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 72.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIMEYASGGE-VFDYLVAHGRMKEK-EARAKFRQIVSAVQYCHQKR-IVHRDLKAENLLLDADMNIKIAD
          .IM.YASGGE..FDY...H.RMK.K.EARAKFRQIVSAVQYCHQK..IVHRDLKAENLLLDADMNIKIAD
Retrocopy IIMKYASGGE<IFDYMIPHRRMKKK>EARAKFRQIVSAVQYCHQKQ<IVHRDLKAENLLLDADMNIKIAD

Parental  FGFSNEFTLGSKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDG-QNLKELRERV
          F.FSNEFTL..KLD.FCGSPPYAA.E..Q..KY....VD.WSLG.ILYTLV...L...G....KELRE..
Retrocopy FCFSNEFTLVTKLDPFCGSPPYAAQEFSQS*KYHELDVDEWSLGIILYTLVNQLLSSGGIESWKELRE--

Parental  LRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIM
          ..GKYRI.FY.ST..E.LLK.FLVLNPIK.G..EQI.KD.W.NAGHEEDEL.PFVEPEL...D.KRIDIM
Retrocopy F*GKYRILFYISTGYEKLLKCFLVLNPIKLGIPEQITKDGWLNAGHEEDELEPFVEPEL---D*KRIDIM

Parental  VGMGYSQEEIQESLSKMKYDEITATYLLLGRKSSELDASDSSSSSNLSLAKVRPSSDLSNSTGQSPHHKV
          VG.GYSQEEIQESLSK.KYDEITAT.LLL.RKS.EL..SDS.S.SN.SLAKVRPSSDLSNST.QSP.HKV
Retrocopy VGVGYSQEEIQESLSKRKYDEITAT*LLLWRKSAELNTSDSNSNSNFSLAKVRPSSDLSNSTRQSPPHKV

Parental  QRSVSSSQKQRRYSDHAGPAIPSVVAYPKRSQTSTADSDLKEDGIPSRKSGGSAGGGKGIAPASPM
          QRS.SS.QKQR.YSDHAGPAIPSV.AY.KRSQ.S.A.SDLKEDGIPS.K.G.SA.GG...A.ASPM
Retrocopy QRSFSSIQKQRAYSDHAGPAIPSVGAYTKRSQISIAISDLKEDGIPSKK*GCSAVGGEAVAQASPM

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_1792 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1792 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000009776	2 retrocopies	retro_itri_1792 , retro_itri_384,