Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatttttccatcttgatgattattccttgtaagattcattgtttttatgtgtataatctcacagttgttcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAG

Basic information

species Zea mays
transcript GRMZM2G013750_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 3
gtgagaatttttccatcttgatgatta-ttccttgtaagattcattg--tttttatgtgtataatctcacagttgt---tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAG
||||||||  |  |  ||  |  |||  || | | ||||||| | ||   ||| |||||| ||||||||| | | |   ||| ||  |||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||| ||||||| |||||||||||||| ||||||||||
gtgagaatcatggctactcaaatattgcttacctataagatttaatgccctttcatgtgtgtaatctcactgatatgcatcaactgtagATATATGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAG
















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|60352441|gb|DN219414.1|DN219414
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|33095283|gb|CF055277.1|CF055277
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|13557648|gb|BG549004.1|BG549004
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|60341151|gb|DN208124.1|DN208124
EST:     ACACACTCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|67017748|gb|CO446497.1|CO446497
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211430132|gb|FL338157.1|FL338157
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211053473|gb|FL477603.1|FL477603
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|149074396|gb|EE162784.2|EE162784
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|18169982|gb|BM339822.1|BM339822
EST:     ACACACGCGTCGAGTTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|31909275|gb|CD650837.1|CD650837
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|32847815|gb|CD987496.1|CD987496
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|120480672|gb|EH210948.1|EH210948
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|40337465|gb|CK371535.1|CK371535
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|149084023|gb|EE173418.2|EE173418
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|149078169|gb|EE166920.2|EE166920
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211157243|gb|FL334276.1|FL334276
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|18175563|gb|BM350832.1|BM350832
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|4753426|gb|AI657336.1|AI657336
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|17930979|gb|BM267939.1|BM267939
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|32824870|gb|CD964592.1|CD964592
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|18166766|gb|BM336605.1|BM336605
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|148945292|gb|EC890506.2|EC890506
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|148945727|gb|EC891006.2|EC891006
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211535625|gb|FL478806.1|FL478806
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTTTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211088675|gb|FL328946.1|FL328946
EST:     CAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: CAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|20803197|gb|BQ294247.1|BQ294247
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|67013990|gb|CO442739.1|CO442739
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|60358562|gb|DN225535.1|DN225535
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|9952312|gb|BE638895.1|BE638895
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211040418|gb|FL321548.1|FL321548
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttgtaagattcattgtttttatgtgtataatctcacagttgttcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAG
                                atctcac  putative branch site (score: 3)
                                            ttcatct  putative PPT
                  tttttatgtgtataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatttttccatcttgatgattattccttgtaagattcattgtttttatgtgtataatctcacagttgttcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG