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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctcgcaaatagctgctgtttgttagaaccataatacagtctcaattttagtagcagaacatttcaaacttccatcactcttactatcttttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA

Basic information

species Zea mays
transcript GRMZM2G098153_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098153_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 3
ttctcgcaaatagctgctgtttgtt-agaaccataatacagtct---caattttagtagcagaacatt--tcaaacttccatcactc-ttactat--cttttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA
          ||  | ||||| |   | ||| ||  |    | |   || || |  | |  | |||||  |  |  |    |   || ||| |||  ||||||  |||||||| |||||||||||||| || || |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||  | |||||||| ||||||||
---------ttatttcctgttggaggaaaactattctgtgttttttgcatttgtcttggttgtacattcatttatttcgtgttggtcattattattgcttttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA
















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|76286915|gb|DV026483.1|DV026483
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|60394964|gb|DN227833.1|DN227833
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|71439970|gb|DR821020.1|DR821020
EST:     AAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: AAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|67015095|gb|CO443844.1|CO443844
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|211168089|gb|FL298967.1|FL298967
EST:     TCAGGAAATCCCTCTGGATCTTANGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|22491340|gb|BU051263.1|BU051263
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCA-TGATCT
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCT
EST: gi|71439969|gb|DR821019.1|DR821019
EST:     AAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: AAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|37399477|gb|CF637068.1|CF637068
EST:     GAAAAGCCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: GAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|74240762|gb|DT648676.1|DT648676
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|166681173|gb|EG102878.1|EG102878
EST:     TGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|87152453|gb|DY397242.1|DY397242
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|211168090|gb|FL298968.1|FL298968
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAG-CTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCCATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|19822328|gb|BQ048352.1|BQ048352
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|101384134|gb|EB814117.1|EB814117
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|93015004|gb|EB640524.1|EB640524
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|76284328|gb|DV023896.1|DV023896
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|101384548|gb|EB814319.1|EB814319
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|67011620|gb|CO440369.1|CO440369
EST:     TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAG

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: 273

TACGTCTCATCCAACCTGTCCCTCGGTGATAGGCAACTCGCTGCGCAATTTCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 181

TACGTCTCATCCAACCTGTCCCTCGGTGATAGGCAACTCGCTGCGCAATTTCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

TACGTCTCATCCAACCTGTCCCTCGGTGATAGGCAACTCGCTGCGCAATTTCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

TACGTCTCATCCAACCTGTCCCTCGGTGATAGGCAACTCGCTGCGCAATTTCAGGAAATCCCTCTGGATCTTAGGATGATCGGGGCAGAAAAGGCTGGATgtatgtgtca ... tttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttagtagcagaacatttcaaacttccatcactcttactatcttttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA
                                 ctcttac  putative branch site (score: 269)
                                 ctcttactatctttt  CT-rich tract
                atttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctcgcaaatagctgctgtttgttagaaccataatacagtctcaattttagtagcagaacatttcaaacttccatcactcttactatcttttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - gctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - -gtagcag