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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 13
gtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
                                                                                || ||| || | ||      | ||  |    | | |  |  |||| |  | ||    | ||| ||| |  |     |   |||  |||    ||||| |||||||||||| |||| ||||||||||||||||||||||||||| |||||||| |
--------------------------------------------------------------------------------actaatttgggtcaga----ttttcatataatatgcattgcattacctgtcatttccttgtt-taaatcata----aaactaatgtttttttttgttttctgcaatcagGAAAGTACAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGACG

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 13
gtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
                                                            | |  |||  || | ||  ||   |||       ||  | | |||  | ||| |  |  || || |  |   |  |||| |||  | |         |||||| || |    |||           |||| || |||||||| |||||||||||||| ||||| |||||||| |
------------------------------------------------------------tgcacctc--tggttatataaatcatgaaaagtctgtaaatgttg--catttatgtgaatgctttgtctac-tgttttgtttacgaat---------gtgtaatttct----ttg-----------cagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAACTTGAAG

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttg---tgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
                                                                                                        || |     |     | | ||    |||    |  |  | | ||||   |   |   |  ||   |    |||| | ||  |   |||| ||||||||||| ||||||||||| || ||||| |||||||| |
--------------------------------------------------------------------------------------------------------gtacagaaatataaatcaataaagcttac---taagacacattttgaaatctagatattaaaaaatcagagttgatttcaacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 13
gtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
                                                                          |||| | |    | ||    |  |||    |||| |  ||||  ||  ||||      ||| |  | ||   |||    |    | | | || | |   || |  |       ||| ||||||||||| |||||||||||||| ||||| ||||||||||
------------------------------------------------------------------------agcatttatcaggggggt----tctcatctcagttcatcgtttccattatttag------tacatcagctaacctttccatccctttctgaattctaaaactgcttgc-------agGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG

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|67015202|gb|CO443951.1|CO443951
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAAGCTATGGTGGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|29544787|gb|CB605395.1|CB605395
EST:     AGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: AGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|67014773|gb|CO443522.1|CO443522
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|67014279|gb|CO443028.1|CO443028
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|9742494|gb|BE518657.1|BE518657
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|32831581|gb|CD971259.1|CD971259
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|211286470|gb|FL080391.1|FL080391
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|211286474|gb|FL080395.1|FL080395
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|31353849|gb|CD438206.1|CD438206
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|149083928|gb|EE173305.2|EE173305
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|211286476|gb|FL080397.1|FL080397
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|211286473|gb|FL080394.1|FL080394
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAARAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|211286478|gb|FL080399.1|FL080399
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
EST: gi|32908579|gb|CF013392.1|CF013392
EST:     TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG                         GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGATG
genomic: TGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG

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: 282

GTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

GTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttct ... ctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG
                              ttttgac  putative branch site (score: 351)
                                      ttgttctct  CT-rich tract
      ttataatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcagGCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATG

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