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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccaatgattaatacaaattaattaattaattatatgtatgtatcaccattaagatagctatggcaacttttgttgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT

Basic information

species Zea mays
transcript GRMZM2G059083_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059083_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 1
---gtgagccaatgattaatacaaattaattaattaattatatgtatgtatcaccattaagatagctatggcaactttt---gttgat-gtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT
      ||| | |  |   |     ||  |  ||  ||   |   |     ||  |   |  || |   | || | |      | ||| |  ||||| ||||||||||||||||||||||| ||||||||||||||||| ||| ||||||||||||||||||| ||||||||||
gtaactagctagtagt--gtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT
















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|78021596|gb|DV489983.1|DV489983
EST:     CAGCGCCCTCGGAGATTTCGGCGACTCC-AGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: CAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|78085945|gb|DV514338.1|DV514338
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|89253046|gb|DY624832.1|DY624832
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|13315987|gb|BG410434.1|BG410434
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|13315986|gb|BG410433.1|BG410433
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|76015965|gb|DT943135.1|DT943135
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|13382263|gb|BG458938.1|BG458938
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTC
EST: gi|13126400|gb|BG316970.1|BG316970
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGTATTAGGCTGGTCTACACCAACGATCAGGGGGAGGT
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTG-AAGAGGCTGGTCTACACCAACGATCAGGGGGAGGT
EST: gi|50328327|gb|CO523453.1|CO523453
EST:     TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACG                         GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACC
genomic: TCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACC

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: 45 (upstream exon), 43 (downstream exon)
Score: 26

CGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

CGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 4

CGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 196

CGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaat ... tgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatatgtatgtatcaccattaagatagctatggcaacttttgttgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT
                                      cttttgtt  CT-rich tract
                   attaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccaatgattaatacaaattaattaattaattatatgtatgtatcaccattaagatagctatggcaacttttgttgatgtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT

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