Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacgggctgcatttgcattttgcatatttgaccattttctagcatacacatattgaagtaacactataaatttatcgattgactgtttatttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC

Basic information

species Zea mays
transcript GRMZM2G106574_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106574_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 3'ss of exon 4
ttcacgggctgcatttgcatt-ttgcatatttgaccattttctagcataca--catattgaagtaacactat-----aaatttatcgattgactgtttattta----tacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGAC--CATTTATGAGATTGTAAC-
            ||   |||  |||||    || |||||||  |  || ||  ||| |  | || | | ||      ||||||||  ||      ||| | |     | ||||||||||| ||||| ||||| || |||||||||||||| ||||||||||| |   ||     | |   | |||     | ||  ||  ||   ||   ||   
------------atggtcatcattgcacgggtggccatttttaaatatgcagtcatttcaatgtgatagtacggtgcaaatttatatatgattcatttttctggtgttgcagAAAATGCTACTTCCGTGTGGTCTGCCTCCTGAGAGAGACGAAGATTGAGGTGGCCTT---CGGGTCTGGCGTTCAGTGTTACTGCAACTACTGGAACCTAGGG
















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|13126102|gb|BG316552.1|BG316552
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32809029|gb|CD961263.1|CD961263
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|14243476|gb|BG841204.2|BG841204
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|76912105|gb|DV164577.1|DV164577
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|4730361|gb|AI649527.1|AI649527
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32846502|gb|CD986183.1|CD986183
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|213169581|gb|FM186027.1|FM186027
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32855389|gb|CD995070.1|CD995070
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32809049|gb|CD961283.1|CD961283
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|33285604|gb|CF075399.1|CF075399
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|60338673|gb|DN205646.1|DN205646
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32806541|gb|CD958775.1|CD958775
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|60358045|gb|DN225018.1|DN225018
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|37391857|gb|CF633173.1|CF633173
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|15080579|gb|BI389110.1|BI389110
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32907954|gb|CF012767.1|CF012767
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|116819876|gb|EC863043.1|EC863043
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|13126508|gb|BG317078.1|BG317078
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|213179135|gb|FM184923.1|FM184923
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|193503211|gb|AM937623.1|AM937623
EST:     GAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: GAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|13126509|gb|BG317079.1|BG317079
EST:     CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|116829615|gb|EC870229.1|EC870229
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|211218119|gb|FL199938.1|FL199938
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|116824059|gb|EC867648.1|EC867648
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|211218118|gb|FL199937.1|FL199937
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32807783|gb|CD960017.1|CD960017
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|32932016|gb|CF036828.1|CF036828
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|84977231|gb|DW475653.1|DW475653
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|33095589|gb|CF055583.1|CF055583
EST:     CCATTGCTGAGAATGAATCTATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTAGTAGTATCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: CCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA
EST: gi|116819488|gb|EC862623.1|EC862623
EST:     TCGGAAGAGAACGTTAC-ATTTCATGCAG                         AAAGTGCTGCTTCCTTGTGGTCTCCCTCCTGAGAGAGATGAAGATTGAGGA
genomic: TCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 252

AGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 230

AGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 115

AGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

AGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataaga ... atttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacacatattgaagtaacactataaatttatcgattgactgtttatttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC
                                          tttattt  CT-rich tract
               taacactataaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcacgggctgcatttgcattttgcatatttgaccattttctagcatacacatattgaagtaacactataaatttatcgattgactgtttatttatacagAAAATGCTGCTTCCTTGTGGCCTCCCTCCTGAGAGAGATGAAGATTGAGGAGCTGTTGCATAGTTTCAGTGTTTCCAATGACCATTTATGAGATTGTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - -gctgcat
- - - - - - - ttgcatt
- - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - -gcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttt