RetrogeneDB ID: retro_itri_89

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393602.1:718171..719665(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022216
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC2A1
• Ensembl ID: ENSSTOG00000021861
• Aliases: None
• Description: solute carrier family 2 (facilitated glucose transporter), member 1 [Source:HGNC Symbol;Acc:11005]

Sequence

>retro_itri_89
ATGGGGACACAGAAGGTGACCCCATCTCTGATCTTTGCTGTCTCTGTTGCTACAATTGGCTCTTTCCAGTTTGGCTACAA
CACTGGAGTCATCAATGCTCCTGAGACTATCATAAAAGACTTTCTCAACTATACTTTGGAAGAGAGATTGGAAGACATTC
CTAGTAAAACATTGCTTACAACCCTCTGGTCCTTGTCTGTGGCCATCTTCTCTGTTGGTGGCATGATGGGCTCCTTTTCT
GTTGGACTCTTTGTCAACCGATTTGGCAGGCGCAATTCAATGCTTATAGTCAACCTGTTGGCTATTGCTGGTGGCTGCCT
CATGGGGTTCTGCAAGATTGCTGAGTCCGTTGAGATGTTAATCCTGGGCCGCTTGATTATTGGACTTTTCTGTGGACTCT
GTACAGGTTTTGTGCCCATGTACATTGGAGAAGTATCTCCTACTGCTCTGAGAGGTGCCTTTGGCACTCTCAACCAGCTG
GGGATCGTCATTGGGATTCTGGTGGCTCAGATATTTGGTCTGGGATTTATCCTGGGATCTGAAGATCTGTGGCCTGTGCT
GTTGGGCTTAACAATTATTCCAGCTATCCTACAAAGTATAGCCCTTCCATTTTGCCCTGAAAGTCCTAGATTCTTGCTCA
TTAATAGAAAAGAAGAGGAGAATGCTAAGAGGATCCTCCAACGGTTATGGGGCACACCAGATGTGAACCAGGATATCCTG
GAACTGAAAGAAGAGAGTGTTAGAATGTCACAAGAAAAGCAAGTCTCTGTGCTGCAGCTCTTTAAGTCACCCAACTACCA
ACAACCCCTCCTCATTTCCATTGTGCTTCAGCTCTCCCAGCAGCTCTCTGGGATCAATGCTGTGTTCTATTACTCAACAG
GAATCTTTAAGGAAGCAGGTGTTGATGAGCCAATATATGCTACCATTGGAGCCGGTGTTGTTAATACTATTTTCACTGTA
GTTTCTCTGTTTCTGGTGGAAAGGGCAGGAAGAAGGACTTTACATATGATAGGCCTTGGAGGAATGGCTATATGTTCCAT
CATCATGACTATTTCTTTGTTATTGAAGGATAACTATAATGCAATGAGCTTTGTCTGTATCACAGCTATCTTGATCTATG
TGGCCTTCTTTGAGATTGGACCAGGCCCTATTCCATGGTTTATTGTGGCTGAACTCTTTGAACAGGGACCACGCCCAGCA
GCCATGGCAGTAGCTGGTTGTTCTAACTGGACCTCCAACTTTTTGGTTGGACTGCTCTTTCTCTCAGCTGCAGCCTATTT
GGGAGCCTATGTTTTTCTTATCTTCGCCACTTTCCTCATTATCTTCCTGGTCTTCACCTTCTTCAAAGTCCCTGAGACCC
GAGGCAGGACTTTTGAGGATATCACACGGGCCTTTGAAGGGCATGGTAATGAGTCCAATAATAGAGCTGGGAAAGGCTCT
GTGGGGGAGATGAACAGCAGCCAGCCTGCTAAGGAGAATACCACCAATGTCTAG

Alignment

ORF - retro_itri_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 95.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKVTGRLMLAVGGAVLGSLQFGYNTGVINAPQKVIEEFYNQTWIHRYGEPILPTTLTTLWSLSVAIFSVG
          .KVT..L..AV..A..GS.QFGYNTGVINAP...I..F.N.T...R.......T.LTTLWSLSVAIFSVG
Retrocopy QKVTPSLIFAVSVATIGSFQFGYNTGVINAPETIIKDFLNYTLEERLEDIPSKTLLTTLWSLSVAIFSVG

Parental  GMIGSFSVGLFVNRFGRRNSMLMMNLLAFVSAVLMGFSKLGKSFEMLILGRFIIGVYCGLTTGFVPMYVG
          GM.GSFSVGLFVNRFGRRNSML..NLLA.....LMGF.K...S.EMLILGR.IIG..CGL.TGFVPMY.G
Retrocopy GMMGSFSVGLFVNRFGRRNSMLIVNLLAIAGGCLMGFCKIAESVEMLILGRLIIGLFCGLCTGFVPMYIG

Parental  EVSPTALRGALGTLHQLGIVVGILIAQVFGLDSILGNEELWPLLLSIIFIPALTQCILLPFCPESPRFLL
          EVSPTALRGA.GTL.QLGIV.GIL.AQ.FGL..ILG.E.LWP.LL....IPA..Q.I.LPFCPESPRFLL
Retrocopy EVSPTALRGAFGTLNQLGIVIGILVAQIFGLGFILGSEDLWPVLLGLTIIPAILQSIALPFCPESPRFLL

Parental  INRNEENRAKSVLKKLRGTADVTRDLQEMKEESRQMMREKKVTILELFRSPAYRQPILIAVVLQLSQQLS
          INR.EE..AK..L..L.GT.DV..D..E.KEES..M..EK.V..L.LF.SP.Y.QP.LI..VLQLSQQLS
Retrocopy INRKEEENAKRILQRLWGTPDVNQDILELKEESVRMSQEKQVSVLQLFKSPNYQQPLLISIVLQLSQQLS

Parental  GINAVFYYSTSIFEKAGVQQPVYATIGSGIVNTAFTVVSLFVVERAGRRTLHLIGLAGMAGCAVLMTIAL
          GINAVFYYST.IF..AGV..P.YATIG.G.VNT.FTVVSLF.VERAGRRTLH.IGL.GMA.C...MTI.L
Retrocopy GINAVFYYSTGIFKEAGVDEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAICSIIMTISL

Parental  ALLEQLPWMSYLSIVAIFGFVAFFEVGPGPIPWFIVAELFSQGPRPAAFAVAGFSNWTSNFIVGMCFQYV
          .L......MS...I.AI...VAFFE.GPGPIPWFIVAELF.QGPRPAA.AVAG.SNWTSNF.VG..F...
Retrocopy LLKDNYNAMSFVCITAILIYVAFFEIGPGPIPWFIVAELFEQGPRPAAMAVAGCSNWTSNFLVGLLFLSA

Parental  EQLCGPYVFIIFTVLLILFFIFTYFKVPETKGRTFDEIASGFRQGGASQSDK
          ....G.YVF.IF...LI.F..FT.FKVPET.GRTF..I...F...G......
Retrocopy AAYLGAYVFLIFATFLIIFLVFTFFKVPETRGRTFEDITRAFEGHGNESNNR

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_89 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_89 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015043	1 retrocopy	retro_dnov_999,
Ictidomys tridecemlineatus	ENSSTOG00000021861	1 retrocopy	retro_itri_89 ,