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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaatgcacactatgcttgtattgtatgaattctccttttcagttcatttttagatgtcattggttccttctgttaattggtaccttatattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 4
ttgaaatgcacactatgcttgtattgt-atgaattctccttttcagttcatttttagatgtcattggttccttctgttaattggtaccttatattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG
   |  |  |    ||  |  |  | | | |  |   |   ||   |||||       |   ||||| | ||| | || ||| ||||||| | | |||||| ||| || || |||||||||||||||||||||   ||||||||||||||||| ||  |||||||||| |||  ||| |||
-ctagttctatttaatagtaatggtctgacgtgtatgcaagttggcttcatgaaatacttctattggctgcttttattgatttgtaccttctttgggccagGTTCCTTGCAGCCTTTATTTAAGCATGTGGAGTCGGGATCAGAGATTCGTGAAAAAGTTATTTGTTTCCTTAAAGATAAG
















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|211179438|gb|FL364366.1|FL364366
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|148969036|gb|EE019749.2|EE019749
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|211444762|gb|FL341640.1|FL341640
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGNGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|71766575|gb|DR964512.1|DR964512
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|60338080|gb|DN205053.1|DN205053
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|211433492|gb|FL365020.1|FL365020
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|148943964|gb|EC889044.2|EC889044
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|211185388|gb|FL309812.1|FL309812
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCT
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCT
EST: gi|211314239|gb|FL336753.1|FL336753
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACGACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|76014976|gb|DT942146.1|DT942146
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|32164953|gb|CD670271.1|CD670271
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|211306674|gb|FL363564.1|FL363564
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|108824166|gb|EC278174.1|EC278174
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|31356580|gb|CD440937.1|CD440937
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|211050490|gb|FL366022.1|FL366022
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|211055963|gb|FL348933.1|FL348933
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGNGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|89761569|gb|DY689527.1|DY689527
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|149105666|gb|EE291222.2|EE291222
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|50326790|gb|CO521916.1|CO521916
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
EST: gi|31358588|gb|CD442945.1|CD442945
EST:     TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAA                         ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG
genomic: TGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTG

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: 624

AGGAAAATGTTGAGCGTGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

AGGAAAATGTTGAGCGTGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 310

AGGAAAATGTTGAGCGTGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 205

AGGAAAATGTTGAGCGTGATGCTGTTCATAAAGCGCTCATGTCCCTTATACGGCAAGATGTTAAAAgtaagattcc ... tattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttttagatgtcattggttccttctgttaattggtaccttatattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG
                            tgttaat  putative branch site (score: 205)
                                          ttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaatgcacactatgcttgtattgtatgaattctccttttcagttcatttttagatgtcattggttccttctgttaattggtaccttatattggccagATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - aatgcac
- - - - - - - -tgcttgt
- - - - - - - - - - - -ttgtatg
- - - - - - - - - - - - - - - - - - - - - - -ttcattt