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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatataagttttcctggtttccaccattgtcacttttgcaaagaagtccttatacttttttta...

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 18
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatataagttttcctggtttccaccattgtcacttttgcaaagaagtccttatacttttttta------
||||||||| || |||||||||||||| || ||||||||||| || || || || ||||||||||||||||||||||| ||||||||||||||||||||||||||  ||||     ||| ||||||  || || | ||   |     || |  || |  |   ||     |||| || |  | |   | | ||| |   |      
AGAACGTGTCCGGCTTAGTTGTTTGCGAGTGCTGCATCAGCTGGCTTCCAGCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaattgcaacccttgttttttctgttttaattttcttggtacttgc--gtattgattttt----tttttacacactaatttctttgcttatccaacagtat

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA17G12950.1 (Glycine max), 5'ss of exon 19
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatata-agttttcctggtttccaccattgtcacttttgcaaagaagtccttatacttttttta------
||||||||| ||||| ||||||||||||||  ||||||| |||||  ||||||| || ||||| || || ||||||||||| ||||  ||||| |||||||||  | |      ||| | || | | ||| | || | || || | |||| |     |  |    || || || ||||| |   | ||| || ||    |       
AGAACGTGTGCGCCTGAGTTGTTTGCGTGTCTTGCATCAACTTGCAGCTAGTACCACCTGTGCGGAGGCCATGGCAGCAACCAGTGTTGGAACACCTCAGgtagctgacaa---gacatgttctataagtatctattaatttacaattttacaatgcttta----tgccagttatgcaatgttctgcttttaattaaactgttatcg

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA05G08040.1 (Glycine max), 5'ss of exon 18
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatataagttttcctggtttccaccattgtcacttttgcaaagaagtcc-ttatacttttttta
||||||||| || || ||||||||||||||  ||||||| |||||  ||||||| || ||||| ||||| ||||||||||| ||||  ||||| |||||||||| |||         |||| | |  |    ||| || || || ||| | |   ||    |    |  |   |     |   |   ||| ||| || |  
AGAACGTGTGCGTCTGAGTTGTTTGCGTGTCTTGCATCAACTTGCAGCTAGTACCACATGTGCTGAAGCCATGGCAGCAACCAGTGTTGGAACACCTCAGgtatcttaaaagacatgttctatatgaatatgttaatt-tacaattttacattcctttatgcgggttatccaatattctgctttttattaaactgttatcg

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT2G26890.1 (Arabidopsis thaliana), 5'ss of exon 18
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt--gtttgacttctttt--tttagtctttacttatataagttttc-ctggtttccaccattgtcacttttgcaaagaagtccttatacttttttta--------
||||||||| |||||||||||||| ||||| || ||||| |||||  ||||||| || ||||| ||||| ||||| ||||| ||||| |||| | | |||||  | || |   |||  || ||  |  | ||       ||  || || |     || |||       ||  |  |       | ||   ||  ||  ||  |||        
AGAACGTGTGCGCCTTAGTTGTTTACGTGTGCTTCATCAACTTGCAGCTAGTACCACATGTGCTGAAGCAATGGCTGCAACTAGTGCTGGAAATGCACAGgttctctactctatttctctcctcctactctaccacacgctgttaaaaatggaaactagttgttggtgttacctatgacatgtataatgactcttaagttgattaaacaccag

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 18
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatataagttttcctggtttccac-cattgtcacttttgcaaagaagtccttatacttttttta
||||||||| ||||||||||||||||||||||| ||||| |||||  |||| || || ||||| ||||||||||||||||| ||||  ||||| ||||| |||| ||      |  ||  | ||||     |  | |||  ||  | ||| |    |  |     ||     | | |||    ||    ||  |   ||  
AGAACGTGTACGCCTTAGTTGTTTGCGTGTTCTACATCAACTTGCAGCTAGCACTACATGTGCTGAAGCTATGGCAGCAACTAGTGTCGGAACACCTCAAgtatgttcagaactatctgttgttttccccatgaaattaattatatattcataacatgaatgtgctggattatcttcaagtttgttggaatgatgaattc-

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|6012267|gb|AW061809.1|AW061809
EST:     GTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAG                         GTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTG
genomic: GTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt ... tgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTG
EST: gi|89761888|gb|DY689721.1|DY689721
EST:     GTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAG                         GTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTG
genomic: GTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt ... tgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTG

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: 45 (upstream exon), 49 (downstream exon)
Score: 83

AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt ... tgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt ... tgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 139

AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt ... tgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttatt ... tgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACGTGTTCGCCTTAGTTGTTTGCGTGTTCTGCATCAGCTTGCGTCTAGTACAACTTGTGCAGAAGCTATGGCAGCAACAAGTGCAGGAACTCCTCAGgtattttattgtttgacttctttttttagtctttacttatataagttttcctggtttccaccattgtcacttttgcaaagaagtccttatacttttttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaagaa