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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgaagtttctttattaatgttaactgaagttttgtttatgtttgcaatctcacgaagcagcattttaatgtttataaggatgtcattctgtaaattttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGG

Basic information

species Zea mays
transcript GRMZM5G840928_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 3'ss of exon 3
gtaactgaagtttctttattaatgttaactgaagttttgtttatgtttgcaatctcacgaagcagcattttaatgtttataaggatgtcattctgtaaattttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGG
                         ||||     |  | ||||| |||||  | |     |  | ||    |   | |   || || | | | | |||  || ||   ||| | || |||  ||| ||||||||||||||  ||||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||
------------------------gtaacattcatggtatttatctttgccgtttatactataatcacaacatcatcttcgagaatctgactttataa--ttactgcacagCGATGGTGAGAGAGAATCTGTTTCTTCTAGAATTCTCACAGAAGTAGCAAAGTGGATGGAGCGCTTTGATTGCATCGTTGTTGGTCCTGGCCTTGGAAGG
















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|76020592|gb|DT947762.1|DT947762
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|71766337|gb|DR964274.1|DR964274
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|211190739|gb|FL216448.1|FL216448
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAA-
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|211152681|gb|FL231436.1|FL231436
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|101395549|gb|EB819702.1|EB819702
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|50323072|gb|CO518198.1|CO518198
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|101385680|gb|EB814888.1|EB814888
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCCTA-GATTCTTACGGGAAGTTGCA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTC-TAAGATTCTTACGG-AAGTTGCA
EST: gi|211190740|gb|FL216449.1|FL216449
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|211190742|gb|FL216451.1|FL216451
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|211190743|gb|FL216452.1|FL216452
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACTGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
EST: gi|76912720|gb|DV164861.1|DV164861
EST:     AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAG                         GGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA
genomic: AGCCCTGAACTAATTGTACATCCAATATTAGAAGAATCTTACAGTGTAAGgtaactgaag ... ttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgaagcagcattttaatgtttataaggatgtcattctgtaaattttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGG
           ttttaat  putative branch site (score: 3)
                                           ttttctt  putative PPT
          attttaatgtttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgaagtttctttattaatgttaactgaagttttgtttatgtttgcaatctcacgaagcagcattttaatgtttataaggatgtcattctgtaaattttcttggcagGGTTGATGAACGAGCATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG