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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattcttacttctgttcccacttaatctggagctatacaggattgcatgctgttatctaaaaattcaactcatggctagactataactcattgtgggtctgctagccaggactaatacgggcctcattgaagcttttttttttgacttgattcggttcttctcttcctactgctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG

Basic information

species Zea mays
transcript GRMZM2G158136_T01
intron # 4
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|16378093|gb|BI992276.1|BI992276
EST:     ATCCTATCAGGGAGCTG-TGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCATATTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|211461323|gb|FL283286.1|FL283286
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAG
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAG
EST: gi|15198911|gb|BI423555.1|BI423555
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAATGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|166681311|gb|EG164840.1|EG164840
EST:     AAAAAGGGAGGAAATTAGAT                         AAACCTACGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAATGTC
genomic: AAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTA-GGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTC
EST: gi|13178302|gb|BG349560.1|BG349560
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTT
EST: gi|60355941|gb|DN222914.1|DN222914
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|76011041|gb|DT938211.1|DT938211
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|71299644|gb|DR785830.1|DR785830
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|13178301|gb|BG349559.1|BG349559
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|148949883|gb|EC895379.2|EC895379
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|148960539|gb|EE011146.2|EE011146
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|60340679|gb|DN207652.1|DN207652
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|149017488|gb|EE154347.2|EE154347
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|60394278|gb|DN227148.1|DN227148
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
EST: gi|91053937|gb|EB164355.1|EB164355
EST:     ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGAT                         AAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT
genomic: ATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 96

GGGCTTTACTGGATCAGACATCCTAGAACTGTGCAAGCAGGCCGCATTCTATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GGGCTTTACTGGATCAGACATCCTAGAACTGTGCAAGCAGGCCGCATTCTATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 175

GGGCTTTACTGGATCAGACATCCTAGAACTGTGCAAGCAGGCCGCATTCTATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 120

GGGCTTTACTGGATCAGACATCCTAGAACTGTGCAAGCAGGCCGCATTCTATCCTATCAGGGAGCTGTTGGACGATGAGAAAAAAGGGAGGAAATTAGATgtgagtattc ... gctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagcttttttttttgacttgattcggttcttctcttcctactgctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG
                             ttcttctcttcctact  CT-rich tract
       ttttttttttgactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattcttacttctgttcccacttaatctggagctatacaggattgcatgctgttatctaaaaattcaactcatggctagactataactcattgtgggtctgctagccaggactaatacgggcctcattgaagcttttttttttgacttgattcggttcttctcttcctactgctgtttcagAAACCTAGGCCCTTGAGACAATCAGACTTGGAGAGAGCCTTGTCAGTGTCTAGAAAGGGCAAGAAGGCTGCAAGTTCAGCACTGCAGTCACCTTTGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG