RetrogeneDB ID: retro_itri_1450

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393492.1:208095..209266(-)
• Located in intron of: ENSSTOG00000010868

Retrocopy information

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

Parental gene information

• Parental gene symbol: LMNB1
• Ensembl ID: ENSSTOG00000003539
• Aliases: None
• Description: lamin B1 [Source:HGNC Symbol;Acc:6637]

Sequence

>retro_itri_1450
GAATCCTGGTCAGAGCTTATGGAGGAGGACTTGGAGTTTTGTAAAAACATGAACAAAGAGGAGATTAATGAGACAAGAAG
AAAGCATGAAACGTGCTTGACAGAGGTGATTCTGGGTGTCAGATCCAGTATGAATACAAGCTGGCTCAAGCCCTTCATGA
GACAAAAGAGCAATATGTGTAAGTGAGGCTGTTCAAGGAAGAGGATGAACAGATTTCCATGCCAAACCTGAGAACCTCCG
ACTGTCCTCAGAGACTAAGACTTCCAGTGTCAACAGTGCCAAGGAAGAACGGAAGGAAGGTCATGTGAGAATGGAAGGCC
TTTCATCTCGACTTTCTAATCTACAATAAAGAGTCTAGAGCATGTTTGGAAATGATTTAAGAGTTGGAAGACTGGTTTGC
TAAAGAAAAGAGACAACTCCTCTCACAAGCTATCTAATGGGGGGGGTGGGGGAGGCAGAAACAAGGGATCAGATGCAGCA
AAAGCTGAATGATTATGAATGACTTCTTCCTGTTAAGCTAGCCCTGGACATGAAAATCATCACTTGTAGGAAACTCTTAG
AAGGAGAGAAAGAGTGGTTGAAACTCTGCACACACTCTTCTTCCCGTGTGAGAGTGTCCCCAGCCTCTTCCAGTCGCAGT
GTGGGCACAGCTAGAGGAAAGCAGGAGAGAGTTGATGTGGAAGAATCAGAGGTCTGCAGAGGTGTGAGTGTCACTCATTC
CACTTCAGCCACTGGGAATGTGTGTGTTGAAGAGATAGATGTGGATGGGAAATGTATTCAGTTGATGAATGCTCCTGAAC
AGGATCCACCAAAGGGAGGCTGGGAGATGATCAGGAAAATTAGAGACACATCAGTCACTTACAAATATGCCTCCAGATAG
GTGCTCCAGGCAGGCCAGACTGTGGCAATTTGGGCTGCAAATGCTGGTGTCACAGTCAGTCCTCCCACCGACCTCATTTG
GAAGAACCAGAATTCTTAGGGCACTGGTGAAGACTTGAAGGTTATTTTGAAAAATTCTCAGGAAGAAGAGGTTGAGCAAA
GTTTTTAAAAACTACCCACACCTGAAGAGGAGGAGGAAGAGAAGGAAGAACCAACCAGGGTGATTGTTGAGAAAGAACTT
TTCCATCAGCCGAGAGCTTCCAGAGCGTTCAGTAGAAGCTGGGCAATTATG

Alignment

ORF - retro_itri_1450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.59 %
• Parental protein coverage: 66.1 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ENRCQSLTEDLEFRKNMYEEEINETRRKHETRLVEV-DSGRQIEYEYKLAQALHEMREQHDAQVRLYKEE
          E.......EDLEF.KNM..EEINETRRKHET.L.EV.DSG.QI.YEYKLAQALHE..EQ....VRL.KEE
Retrocopy ESWSELMEEDLEFCKNMNKEEINETRRKHETCLTEV<DSGCQIQYEYKLAQALHETKEQY-V*VRLFKEE

Parental  LEQT-YHAKLENARLSSEMNTSTVNSAREELMESRMRIESLSSQLSNLQ-KESRACLERIQELEDLLAKE
          .EQ...HAK.EN.RLSSE..TS.VNSA.EE..E...R.E.LSS.LSNLQ.KESRACLE.I.ELED..AKE
Retrocopy DEQI<FHAKPENLRLSSETKTSSVNSAKEERKEGHVRMEGLSSRLSNLQ>KESRACLEMI*ELEDWFAKE

Parental  -RDNSRRMLTDKEREM-AEIRDQMQQQLNDYEQLLDVKLALDMEISAYRKLLEGEEERLKLSPSPSSRVT
          .RDNS...L........AE.RDQMQQ.LNDYE.LL.VKLALDM.I...RKLLEGE.E.LKL....SSRV.
Retrocopy >RDNSSHKLSNXXXXX>AETRDQMQQKLNDYE*LLPVKLALDMKIITCRKLLEGEKEWLKLCTHSSSRVR

Parental  VSRASSSRSVRTTRGKRKRVDVEESEASSSVSISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGW
          VS.ASSSRSV.T.RGK..RVDVEESE....VS..HS.SATGNVC.EEIDVDGK.I.L.N..EQD.P.GGW
Retrocopy VSPASSSRSVGTARGKQERVDVEESEVCRGVSVTHSTSATGNVCVEEIDVDGKCIQLMNAPEQDPPKGGW

Parental  EMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEV
          EMIRKI.DTSV.YKY.SR.VL.AGQTV.IWAANAGVT.SPPTDLIWKNQNS.GTGED.KVILKNSQ.EEV
Retrocopy EMIRKIRDTSVTYKYASR*VLQAGQTVAIWAANAGVTVSPPTDLIWKNQNS*GTGEDLKVILKNSQEEEV

Parental  AQRSTVFKTTIPEEEEEE-EEPTGVVVEEEIFHQQGSPRSSNKSCAIM
          .Q.....K...PEEEEEE.EEPT.V.VE.E.FHQ....R....S.AIM
Retrocopy EQ--SF*KLPTPEEEEEEKEEPTRVIVEKELFHQPRASRAFSRSWAIM

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_1450 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1450 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	ENSSTOG00000003539	1 retrocopy	retro_itri_1450 ,