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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattggccacaccagttccaaaaggtggatttgggtcatccgtactcttctccaatgtaccaaatgccgtactaatttgttgttgtcttctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG

Basic information

species Zea mays
transcript GRMZM2G007260_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007260_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 4
gtattggcca-caccagttccaaaaggtggatttgg-gtcatccgtactcttctccaatgtaccaaat---gccgtactaatttgttgttgtcttctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG
     | | |  |   | |           | |||  ||| |||   || |  |||   || ||| ||   ||    ||  ||   | ||| ||| | | ||||||||||||| ||||| ||||||||||| || ||||| ||||| |||||||||||| ||||||||||||||||||| ||||||||||||||||| || ||| 
-----gacaaataatggcttgggggaccatagttgatgtcttcctgcctgtaatcctcagttccacattgagcttagctgtttctgttttgccttttatctgcagTCCCTGCTCTGTGATCCAAACCCAAACTCCCCTGCAAACTCCGAAGCAGCCAGACTGTTCAGCGAGAACAAGCGCGAGTACAACCGCAAAGTCCGCGAGA

upper sequence: GRMZM2G007260_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 4
-gtattggccacaccagttccaaaaggtggatttgggtcatccgtac-tcttctccaatgtaccaaatgccgtactaatttgttgttgtcttctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG
 |  |  |      | |   |       | ||||| | | |   ||| ||  |  ||| |   |  |   ||   | || |  |         |   |||||||  ||||||| ||||||||||| ||||| || || ||||| || || ||| | |||| |||||||||   ||||||||||||||| |  || || ||| 
agcttgagattggtcggcgtcttctttggcatttgcggc-tgaatacgtcgacgacaacgatgcgtagagcgagattatctaatac-acggctttgatgcagTCTTTGCTGTGCGACCCAAACCCGAATTCACCAGCGAACTCGGAGGCTGCCCGCATGTACAGCGAGAATCGGCGTGAGTACAACCGGAGGGTACGCGAGA
















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|37397476|gb|CF636037.1|CF636037
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|110947584|gb|EE167741.1|EE167741
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|18168064|gb|BM337904.1|BM337904
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|37377294|gb|CF625238.1|CF625238
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|12972475|gb|BG268000.1|BG268000
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|18168754|gb|BM338594.1|BM338594
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|94474209|gb|EB703167.1|EB703167
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|32857587|gb|CD997268.1|CD997268
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|149112232|gb|EE191288.2|EE191288
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|94474208|gb|EB703166.1|EB703166
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|113703398|gb|EE680902.1|EE680902
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|18179315|gb|BM380525.1|BM380525
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTTTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|78122431|gb|DV540815.1|DV540815
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
EST: gi|32857308|gb|CD996989.1|CD996989
EST:     ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG                         TCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC
genomic: ACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCC

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: 39 (upstream exon), 49 (downstream exon)
Score: 601

TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 718

TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 797

TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 720

TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctca ... ctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttctccaatgtaccaaatgccgtactaatttgttgttgtcttctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG
                         tactaat  putative branch site (score: 720)
                                   ttgttgtcttctcttt  putative PPT
                         tactaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattggccacaccagttccaaaaggtggatttgggtcatccgtactcttctccaatgtaccaaatgccgtactaatttgttgttgtcttctctttgcagTCCCTGCTGTGTGACCCAAACCCAAATTCTCCTGCCAACTCTGAAGCAGCCAGAATGTTCAGCGAGAACAAGCGTGAGTACAACCGCAAAGTTCGTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - caccagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt