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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 4
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 4
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 4
gtatgtctctgggctctggcc-----atgtttatg-------ttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttgg--ttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
|||| ||| || ||| |         ||| ||||        || |  ||| | | |    | || | || |   || |||| | ||  |    |||||| |  |   |||   ||||  ||   ||| |||||| ||||||||||||||||| |  ||||| |||||||||||||| |||||||||||||||||||||||||||||||| || || ||||| |||| ||| |
gtatatctttgcgcttttatgtgcaaatgcttatttaatccctttatctgcctttcagggtatttggctattttgttgcctagtttcactagcattttcttattt---taaattctgtcatgtatttgagcagTTCAAGCAAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaata-cctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
                ||||| | ||| | | || ||  ||   | |||  ||  | |   ||  || |   ||    ||  | |||     |    | ||   | | |||  ||| |||||||| ||||||||||| || |   | ||||| || ||||| || |||||||| |||||||| ||||| || ||||| ||||| |||||||||| |||  
--------------gttggcc-tatttctctgcagat--ttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
gtatgtctctgggctctggccatgtttatgt--tcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
                  |  |  ||| ||     | ||| |||  | |  | |   ||    | ||   ||   ||    |  |      |   |   | |   |   |   | ||  ||||||||||||| ||||| || || || ||||| || |||||||| || ||||| |||||||||||||| |||||||||||||| |||||||||| |||  
------------------gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagt--ttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
         || | | ||      |  ||||| |       || ||  || ||    ||| |  |  ||  | || |   | |     | | | |    ||| ||  | |    |  ||||||||||||| ||||| || || || ||||| || |||||||| || ||||| |||||||||||||| |||||||||||||| ||||| |||| |||  
--------gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaa--gtctaaagactaattcagtgtacttgcatgg----tatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
                      ||  ||| ||    || ||   ||| |  ||||||||||  || |  |  ||| ||    |    | |   |    |||  ||  |    |||||||||||| ||||||||||| || || || |||||||||||||||||  | || || || ||||| |||||||| ||||||||||| ||||| |||| |||| 
--------------------gttgaatatttttttgtggtttgaaaagatatttgttactgc-ttccaaagcctctatttcgtgcagtgagtaatt--atatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
                  |  |  |  |   |||| | | | |  |      ||||    ||||||  |    |  ||||||| || ||       ||||         |  | | |||||||| ||||||||||| || ||    ||||||||||||||||| ||  ||||||||||||| ||||| |||||||| ||||| ||||| |||| |||| 
------------------gtgagatacacactcaa-tacatgtatatggttcttgt----ggatttgtt---tttcatcatttattttctgagttttaatg--------gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA

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|29167975|gb|CB411235.1|CB411235
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211458486|gb|FL255599.1|FL255599
EST:     GATTTGATATGATCTGCAGTGGAAGGGACTAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGGCCA-CAAGCTTGATTTGGATGGACTTGT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGG-CCAACAAGCTTGATTTGGATGGACTTGT
EST: gi|149083748|gb|EE173108.2|EE173108
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTG
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTG
EST: gi|148953762|gb|EC899129.2|EC899129
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211458479|gb|FL255592.1|FL255592
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211458477|gb|FL255590.1|FL255590
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACNGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|5268364|gb|AI770328.1|AI770328
EST:     GATTTGATATGATCTGCAGTGGAAGGGACCAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTG
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTG
EST: gi|211462254|gb|FL324872.1|FL324872
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211179440|gb|FL364368.1|FL364368
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGNT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211540563|gb|FL329390.1|FL329390
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|149083929|gb|EE173306.2|EE173306
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211187935|gb|FL314087.1|FL314087
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGA
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGA
EST: gi|211458484|gb|FL255597.1|FL255597
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTNGGATGGACTTGT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTT-GGATGGACTTGT
EST: gi|211336170|gb|FL255578.1|FL255578
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACGGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211458364|gb|FL364597.1|FL364597
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|149103124|gb|EE288493.2|EE288493
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|20803238|gb|BQ294288.1|BQ294288
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCT
EST: gi|31354738|gb|CD439095.1|CD439095
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|211334009|gb|FL255568.1|FL255568
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCCACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
EST: gi|149105648|gb|EE291200.2|EE291200
EST:     GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG                         TTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT
genomic: GATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTT

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), 47 (downstream exon)
Score: 347

GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 380

GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAGgtatgtctct ... ggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
            atcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG