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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaaaatctttttctgatgctctcatgtttttttcttcctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA

Basic information

species Zea mays
transcript GRMZM2G461793_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g17040.1 (Oryza sativa), 3'ss of exon 2
-ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaaaatctttttctgatgctctcatgtttttttcttcctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA
 || |||    |||  |  ||||  | |       |    |  ||   | | | || |  |  |  | |    || |  | ||  |     ||   ||||||||||||||| || || |||||||| || |||||||||||||  ||||| |||||||||||||| |||||||| || | |||||||||||||||||| ||
attctttcccatatagaa-attatgcctatcatctgatcttttttgttacattattctgtttgtattttgtatttatccttttttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCTCATCATCCAAATAAATTATGGGAGAGGGTCAAACTACCAAGGAATTATGAGAAAGCAATTGA

upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 2
ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaaaatctttttctgatgctct--catgtttttttcttcctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA
 || || ||||      | ||   |   |     |  ||   |   || | | ||||| | |   |||      ||| | |||   |     ||   ||||||||||||||| || || |||||||| || |||||||| ||||| || ||||||||||||||||| |||||||| || |  ||||||||||||||||||||
attgttttgctcccggttctt--tcccaacttatgtataccatcttaatattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA

upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0030g01480.t01 (Vitis vinifera), 3'ss of exon 12
ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaa---aatctttttctgatgctctcatgtttttttctt-cctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA
   | ||   |||| | | ||  |  |  |   |   ||    |  | |   || || | | ||     || |||||  |   |   |||      || ||||||  | || ||||| || |||||||||   |||||||| ||| |||||||||||||||||||  | || ||| ||||    || || |  || ||  | ||
---tgtgatttatggattgtttcctctttattaaatttagttctttagatcaaagctgtatgtggctgact-atgttaatgattggtctctggttcttgtgcagGAGTGTTTTATCTATACATGAAAACCATTGAAAGAGCCCATATGCCAAACAAATTATGGGAACGGGTTAAATTGCCACGAAACTACGGAAAGGCTCTTGA

upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g09220.t01 (Vitis vinifera), 3'ss of exon 3
ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaa---aatctttttctgatgctctcatgtttttttctt-cctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA
   | ||   |||| | | ||  |  |  |   |   ||    |  | |   || || | | ||     || |||||  |   |   |||      || ||||||  | || ||||| || |||||||||   |||||||| ||| |||||||||||||||||||  | || ||| ||||    || || |  || ||  | ||
---tgtgatttatggattgtttcctctttattaaaattacttctttagatcaaagctgtatgtggctgact-atgttagtgattggtctctggttcttgtgcagGAGTGTTTTATCTATACATGAAAACCATTGAAAGAGCCCATATGCCAAACAAATTATGGGAACGGGTTAAATTGCCACGAAACTACGGAAAGGCTCTTGA

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|93012902|gb|EB638422.1|EB638422
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|71330256|gb|DR801876.1|DR801876
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|148939429|gb|EC883983.2|EC883983
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211291475|gb|FL225666.1|FL225666
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTGTTTTCTATCTGTATATGAAAACCGCTGAAAGGGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211345141|gb|FL350534.1|FL350534
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211248875|gb|FL353267.1|FL353267
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTGTTTTCTATCTGTATATGAAAACCGCTGAAAGGGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|31355775|gb|CD440132.1|CD440132
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTGTTTTCTATCTGTATATGAAAACCGCTGAAAGGGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211008090|gb|FL365103.1|FL365103
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|76932105|gb|DV172945.1|DV172945
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211373401|gb|FL472199.1|FL472199
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTGTTTTCTATCTGTATATGAAAACCGCTGAAAGGGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|29130836|gb|CB381540.1|CB381540
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|148946083|gb|EC891379.2|EC891379
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211286714|gb|FL323329.1|FL323329
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|91872818|gb|EB402775.1|EB402775
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211526412|gb|FL361960.1|FL361960
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|148987550|gb|EE031415.2|EE031415
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|33467372|gb|CF244421.1|CF244421
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|71431373|gb|DR812423.1|DR812423
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTTCTATCTGTATATGAAAACCGCCCGAAAGAGCTCATCTGCCAAA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTT-CTATCTGTATATGAAAACCGCC-GAAAGAGCTCATCTGCCAAA
EST: gi|94477914|gb|EB706872.1|EB706872
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|211360103|gb|FL362300.1|FL362300
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|71322072|gb|DR797726.1|DR797726
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|31355774|gb|CD440131.1|CD440131
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTGTTTTCTATCTGTATATGAAAACCGCTGAAAGGGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
EST: gi|148953458|gb|EE152961.2|EE152961
EST:     CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAG                         GTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA
genomic: CTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACA

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: 173

GGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 140

GGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 167

GGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 154

GGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGGGATCATGAAGgtgatcacca ... ggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaaatctttttctgatgctctcatgtttttttcttcctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA
           ttctgat  putative branch site (score: 154)
                        atgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaaaatctttttctgatgctctcatgtttttttcttcctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - -tgtgcta
- - - - - - - - - - - - - - - - - - - -tgcttac