Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcttgtatgagtatttattgcagttgaataattggtgttcctcttccttagataataatcaatccacctaactgatgctgaaatgcctttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG

Basic information

species Zea mays
transcript GRMZM2G063253_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 3
ggtcttgtatgagtatttattgcag---ttgaat--aattggtgttcctcttccttagataataatcaatccacctaactgatgctgaaatg-cctttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
      | |  |   |||||||||    || | |  ||||| ||| || ||| |||  | | |||||||||||||||||| |||| |||||| ||||||  | |||||||| |||||||| |||||||| |||||||| ||||| ||||| |||||||||||||||||||||||
-----agcacaacattttattgcaagcatttatttcaattgatgtgcc-ctttcttccacactaatcaatccacctaacttatgccgaaatgtcctttatgtctagATGACAAAGCTGGCTATCATCCCATGCACTGTTATTTTGGAGACTCTTTTCTTCAGGAAGAAGTTCAG

upper sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 2
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
ggtcttgtatgagtattt--attgcagtt---gaataat-tggtgttcctcttccttagataataatcaatccacctaactgatgctgaaatgcctttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
      ||||   | |||  ||| |||||   | || || || | | | | ||       |  |  || |     |||||  || ||    | || || |   ||||||||||| || || |||||||| ||||||||  | || ||||| || ||||||||||| ||||||||
------gtatagctttttccatttcagttactgcatgatgtgatatccatttttaactagtgttgttctaatt-tctaacccat-cttctgttccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG

upper sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 4
-------ggtcttgtatgagtatttattgcagttgaat----aattggtgttcctcttcc--ttagataataatcaatcca-------cctaactgatgctgaaatgcctttaaattt-agATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
           |  | ||| ||||   | |  ||  ||    || |  || |||| | ||  ||   |  |  ||||   |       |  |||| ||| |  | ||  | |  |||  ||||||| |||||||||||||| || || |||||  | || ||||| ||||||||||||||||| |||||
gtaaaattaattcttctgaatattccctactattacatgttcaacttttggtcctttgccatttcagtgtttctcaagagagtggtttctgaacttatgttatattgtttgtgtattccagATGACAAAGCTGGCAATCATTCCCTGTACTGTACTCTTGGAGACCCTTTTCTTCAGGAAGAAATTCAG

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|148972178|gb|EE023052.2|EE023052
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|149014408|gb|EE044009.2|EE044009
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|149036981|gb|EE155219.2|EE155219
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|76915217|gb|DV165886.1|DV165886
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|148983177|gb|EE029121.2|EE029121
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|211175084|gb|FK975381.1|FK975381
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|91049957|gb|EB160375.1|EB160375
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|149015304|gb|EE045114.2|EE045114
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|8576977|gb|BE129614.1|BE129614
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGGTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCATGCAC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCAC
EST: gi|148974636|gb|EE025433.2|EE025433
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|78078452|gb|DV506865.1|DV506865
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|148995836|gb|EE035071.2|EE035071
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|74244914|gb|DT652828.1|DT652828
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|71304057|gb|DR788150.1|DR788150
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|149106695|gb|EE188591.2|EE188591
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|74242511|gb|DT650425.1|DT650425
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
EST: gi|148930581|gb|EE285235.2|EE285235
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtacgtagct ... ttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttagataataatcaatccacctaactgatgctgaaatgcctttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
                                        tgccttt  CT-rich tract
     tagataataatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcttgtatgagtatttattgcagttgaataattggtgttcctcttccttagataataatcaatccacctaactgatgctgaaatgcctttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT