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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA

Basic information

species Zea mays
transcript GRMZM2G124353_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 4
gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA
|||| |  ||| |   ||   ||| || |          |||| |||| | |  ||| ||||  |           ||   ||| ||||||    | | || ||||||||||||||  | |     ||||||| ||||||||||| ||||||||||||||||||||  |||||||||||||||||| ||| || ||||||||||| |||||||| ||||||||||||||||
gtatgattttttatatgatactttttaca----------taatcgaaagatt--gtagctttcctcagct--ttttatctgaaagaacttactgatatggcgatcttgttgatacatgaacatgaatgtagGGCGTGGGAGGTGCAGTTGAACTAGCTCCTGGATATTTAAAGTTAGCTTATGACACTGTCCGGAAGGCTGGTGGTGTTTGTATAGCTGATGAAGTCCAGA

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 4
gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA
          || | |  ||||  || |  || |  |  |   | || |     ||    ||| |    | || ||  | |   |   ||  |  || |    || |  ||  |   | |||      ||||| |  ||||| || |||||||| || ||||| ||||||||  | |  ||||||||||| | ||| |||||||| || || |||||||||||||| ||  
-------gcatgtataatccatccatca--tgtttaattt--ctaaacttcagagtggtatttatagccacacacaccttagtgtggttttcctatgactttttcctcatgtcatggcttcttc----tagGGAGCTGGAGGAGCAGTTGAACTGGCACCTGGGTACCTAAAACTGGTCTATGACATTGTACACAAAGCTGGTGGTGTCTGCATTGCTGATGAAGTGCAAT

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G36000.1 (Glycine max), 3'ss of exon 4
gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA----
           | | |  ||||  || |  || |  |  |   | || |     ||    ||| |    | || ||  | |   |   ||  |  || |    || |  ||  |   | |||      ||||| |  ||||| || |||||||| || ||||| ||||||||  | |  ||||||||||| | ||| |||||||| || || |||||||||||||| ||      
-----------gtataatccatccatca--tgtttaattt--ctaaacttcagagtggtatttatagccacacacaccttagtgtggttttcctatgactttttcctcatgtcatggcttcttc----tagggagCTGGAGGAGCAGTTGAACTGGCACCTGGGTACCTAAAACTGGTCTATGACATTGTACACAAAGCTGGTGGTGTCTGCATTGCTGATGAAGTGCAATGTGG

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 4
gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA
                      || |    || |  ||| ||    |  ||     || |  || ||    || |  || || ||||       | ||| | ||    ||     | ||| | | ||  |||| || ||||| ||||| ||| | |||||||| ||| ||||||  | |||||| ||||| ||||| |||||||| || || ||||||||||||||||| |
---------------------gtttttgtttgtttaaacaaacc--atcaagtgaaatttagtgatttaccactctcttgaacataa-------tcgtcaccatgccatt-----atcatttttacttcagGGGGTCGGAGGAGCTGTAGAATTGGCTCCTGGTTACTTAAAGTCGGTTTATGAAATTGTTCGCAACGCTGGTGGTGTATGCATTGCTGATGAAGTCCAAA

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 4
gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaa-ataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA
                |  |||   | || | ||    ||  ||||  |  ||  ||  || | | |    ||   |||  || || |   || |   |  |||  || |   |     |      || ||||| |||||||| || || ||| |||| ||||||||| | ||  | | ||||||||| || ||||||||||| || |||||||||||||| ||||| || |
----------------gttcat--gttaattact----ctttttgaggtg-taaatacattgtttcttactacatgattggaacattatggattcc-atttcaaaattctcattttggaaa----actttagGGAGTGGGAGGAGCAGTGGAATTAGCCCCTGGATACTTGAAACTGGTTTATGACATCGTCCGCAAGGCTGGGGGTGTTTGTATTGCTGACGAAGTGCAAA

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|67034943|gb|CO463476.1|CO463476
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAG                         GGTGTGGGAGGGGCTGTTGAACTAGCTCCTGGATACCTANAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|149042716|gb|EE047231.2|EE047231
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCCA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|211311887|gb|FK975958.1|FK975958
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|148965746|gb|EE016621.2|EE016621
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|30031577|gb|CB833428.1|CB833428
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|6626596|gb|AW258128.1|AW258128
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|44682053|gb|CK787101.1|CK787101
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|94472312|gb|EB701270.1|EB701270
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|13558145|gb|BG549501.1|BG549501
EST:     CTTATGGAAGTTCAGGAAGGGT-GCAGGCTTCATTGCAGAAACATTCCAA                         GGTGTGGGAGGTGCTGT-GAACTAGCTCCTGGATACCTAAAGT-AGCT-AT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
EST: gi|148955020|gb|EC900523.2|EC900523
EST:     CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCGA                         GGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT
genomic: CTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTAT

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: 472

TTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 853

TTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1094

TTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 506

TTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATGGAAGTTCAGGAAGGGTTGCAGGCTTCATTGCAGAAACATTCCAAgtataaactt ... tctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA
                                        ccatctct  CT-rich tract
     aaataacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaactttgaacagaccatttataaaatgctagaactaattgaaataatatgtatcttttgtttataaacccaattcaaaataacttatccttgtcgcaatcttgttgatacaccatctctgctgtagGGTGTGGGAGGTGCTGTTGAACTAGCTCCTGGATACCTAAAGTTAGCTTATGACATTGTGCGCAAGGCTGGTGGCGTTTGTATTGCTGATGAAGTCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT