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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatgattgtttactgccgtttatattcttagctgtgccatgtcaattttccttaagaaacgaatcctgtgataattttttacggttgctgaatgc...

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 25
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 25
GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatgattgtttactgccgtttatattcttagctgtgccatgtca----attttccttaagaaacg-aatcctgtgataattttttacggttgctgaatgc
||||| |||||||||||||||||||||||||| ||||||||||||||| |||| ||||||||||||||||||||||| ||    ||  |||  | ||||  || || | |  |     | |    |    |  |||||| |   || |||   | |  || | ||  |  ||     
GATAATAACCCGAACAATCTGGTTGCATGCACTACATTCTTTTCTGAAACAACCCGTGCCATGCTTTGTCTGgtaagtatatcggtgaactttcctttaatttgttcgtttagttgcatgagaacacacactctaagaatcatgatgctgaattcaacttgttcgtattatg-----

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 25
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 5'ss of exon 23
----------------------------GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatgattgtttactgccgtttatattcttagctgtgccatgtca----attttccttaagaaacg-aatcctgtgataattttttacggttgctgaatgc
                            ||||| |||||||||||||||||||||||||| ||||||||||||||| |||| ||||||||||||||||||||||| ||    ||  |||  | ||||  || || | |  |     | |    |    |  |||||| |   || |||   | |  || | ||  |  ||     
CACTTTTGAACTTCTTGTTCCTTTTTAGGATAATAACCCGAACAATCTGGTTGCATGCACTACATTCTTTTCTGAAACAACCCGTGCCATGCTTTGTCTGgtaagtatatcggtgaactttcctttaatttgttcgtttagttgcatgagaacacacactctaagaatcatgatgctgaattcaacttgttcgtattatg-----
















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|211479461|gb|FL404982.1|FL404982
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCNTCTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|211430870|gb|FL250418.1|FL250418
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|37395386|gb|CF634973.1|CF634973
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|40336758|gb|CK370828.1|CK370828
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAATAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|113704027|gb|EE681531.1|EE681531
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|67018440|gb|CO447189.1|CO447189
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|211430871|gb|FL250419.1|FL250419
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
EST: gi|213169610|gb|FM186192.1|FM186192
EST:     TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG                         ATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT
genomic: TTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTT

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: 48 (upstream exon), 47 (downstream exon)
Score: 124

GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTTGCCTCGGGCGACCAATATTTGACATTCGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 98

GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTTGCCTCGGGCGACCAATATTTGACATTCGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 131

GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTTGCCTCGGGCGACCAATATTTGACATTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatga ... ttctttccagATACGAGTTGAAACAGATCCACAAGACAGGACCCAACTGCGGCTAACAGTTGCCTCGGGCGACCAATATTTGACATTCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTGgtaagcatgattgtttactgccgtttatattcttagctgtgccatgtcaattttccttaagaaacgaatcctgtgataattttttacggttgctgaatgc

- - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacgaa