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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgtccctgtgccagctccggctagtgttttattcccatgctgcagtttctacatctttatgtggcaagtcatatacattattagtctacatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG

Basic information

species Zea mays
transcript GRMZM2G097226_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 2
tttcgtccctgtgccagctccg-gctagtgttt-tattcccatgctgca-gtttctacatctttatgtggcaagtcatatacattattagtctacatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG
| || || || || ||| | || | || || | | || || |||||||| || | || || | | ||| | ||||||||||||||||||| || ||||||||||| | |||||||| ||||||||||||||||| |||||||||||||| ||||||
-aggggaaaaatgacatttctatattaaaatttgtttttctttgttgggcaccttgatatggcaat-tggcaagttatctgcaacat-attttacttattcagATGACTGTCCGTGAAGCGCTGAACTCTGCACTCGATGAAGAAATGTCTGCTGATCCTTCTGTTTTTCTGATGGGTGAAGAG
















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|78122124|gb|DV540508.1|DV540508
EST:     CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG                         ATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
genomic: CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
EST: gi|211069303|gb|FL193602.1|FL193602
EST:     CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCTGCGGCGAAGGAG                         ATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
genomic: CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
EST: gi|32799904|gb|CD952140.1|CD952140
EST:     CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG                         ATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
genomic: CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
EST: gi|91057168|gb|EB167586.1|EB167586
EST:     CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG                         ATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT
genomic: CAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCT

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: 369

ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 376

ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 869

ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAGgtgaggcgcc ... acatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttctacatctttatgtggcaagtcatatacattattagtctacatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG
                          tcatatacattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgtccctgtgccagctccggctagtgttttattcccatgctgcagtttctacatctttatgtggcaagtcatatacattattagtctacatgttcagATGACTGTCCGTGATGCATTGAACTCTGCATTGGATGAAGAGATGTCTGCTGATCCTTCCGTTTTTCTGATGGGAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - -tgccagc
- - - - - - - - - - - gctagtg
- - - - - - - - - - - - - - - - - - - - -gctgcag