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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatatgatctatatgctcttctccctttccgagactaccttattttactgagaggcttatccctaaaccttgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG

Basic information

species Zea mays
transcript GRMZM2G023232_T01
intron # 9
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|4966541|gb|AI691397.1|AI691397
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|211440101|gb|FK975188.1|FK975188
EST:     CCGGTCCTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|4647435|gb|AI622510.1|AI622510
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|91048554|gb|EB158972.1|EB158972
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|5688777|gb|AI941792.1|AI941792
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCNCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|21391185|gb|BQ529234.1|BQ529234
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|4647591|gb|AI622666.1|AI622666
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|67032981|gb|CO461730.1|CO461730
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGANACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTGCTAGGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|60394852|gb|DN227721.1|DN227721
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTTTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|211440104|gb|FK975191.1|FK975191
EST:     CCGGTCCTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|78106113|gb|DV524531.1|DV524531
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|24768622|gb|CA403751.1|CA403751
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|37375721|gb|CF624316.1|CF624316
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|83278270|gb|DV942278.1|DV942278
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|61119613|gb|DN560574.1|DN560574
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|211139744|gb|FL308469.1|FL308469
EST:     CCGGTCCTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGNAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|21390042|gb|BQ528091.1|BQ528091
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|32943975|gb|CF048794.1|CF048794
EST:     CTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: CTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|60354460|gb|DN221433.1|DN221433
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|4624362|gb|AI615195.1|AI615195
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|67022747|gb|CO451496.1|CO451496
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|211440103|gb|FK975190.1|FK975190
EST:     CCGGTCCTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|32823844|gb|CD963566.1|CD963566
EST:     TAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|166434543|gb|EG218599.1|EG218599
EST:     AAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: AAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|21395211|gb|BQ539641.1|BQ539641
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAGGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|5608144|gb|AI901811.1|AI901811
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACNCTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|67034483|gb|CO463033.1|CO463033
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|78023706|gb|DV492093.1|DV492093
EST:     GAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: GAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|211440106|gb|FK975193.1|FK975193
EST:     CCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGACAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCACAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
EST: gi|6022408|gb|AW067336.1|AW067336
EST:     TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAG                         GTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC
genomic: TCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 741

GGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 405

GGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 560

GGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 508

GGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTGACCTTAAGAAGAAAGCTGAAACACTTGATAGgttagcatat ... tgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccgagactaccttattttactgagaggcttatccctaaaccttgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG
              ttattttact  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatatgatctatatgctcttctccctttccgagactaccttattttactgagaggcttatccctaaaccttgatctacagGTTCTGCAAGCCGATCATGACGAAACCGAAGCCAGCTCCTAAGCCGCAGACTCCGCCTGTGGCAGAAAACCAAGCTCCTGAGCCTCAGACACCAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG