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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatataactgctatttatagtcttgttttctgttgattactatgagcatggtgttttggtgttgtattcaatgttctgagctatccttaactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA

Basic information

species Zea mays
transcript GRMZM2G022563_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 3'ss of exon 3
--attaatataactgctatttatagtcttgttttctgttgattactatgagcatggtgt-tttggtgttgtattcaatgttctgagctatccttaactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA
  ||  ||||   |  |||| |      || | |||  || |   |   |  | | |||      | ||| ||| ||        |  |   |  |  ||||||||||| | || ||||| ||| |||| || ||||| |||||||| || ||||| |||||||||||| |  | || ||||| || |||||||| |||||||
aaatgtatattgat-ttattaacttgactgctctcttatgttcttttaaaaaaagatgtgcacaattttgcattaaaaacatctggtaaaaat--ataaacagGTGCTGGCGGAGGTGGGATGCGCAAATGCATTTGGCTTTGATATCACTGCTGCATGTAGTGGGTTTATTATTGGTTTAATTACGGCTACTCGTTTTATCA
















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|71430696|gb|DR811746.1|DR811746
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|76921158|gb|DV168472.1|DV168472
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|89756348|gb|DY686398.1|DY686398
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|71429949|gb|DR810999.1|DR810999
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|76291106|gb|DV030674.1|DV030674
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|149095842|gb|EE181493.2|EE181493
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|149105057|gb|EE290536.2|EE290536
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAN                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|78121840|gb|DV540224.1|DV540224
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|148935022|gb|EC879064.2|EC879064
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
EST: gi|101397488|gb|EB820667.1|EB820667
EST:     TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAG                         GTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT
genomic: TTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 100

TCAAAGGGCACTTGAGATGGCCGGAGTAAAAGCTGAAGATGTCGACCTCGTTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

TCAAAGGGCACTTGAGATGGCCGGAGTAAAAGCTGAAGATGTCGACCTCGTTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 50

TCAAAGGGCACTTGAGATGGCCGGAGTAAAAGCTGAAGATGTCGACCTCGTTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA


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

TCAAAGGGCACTTGAGATGGCCGGAGTAAAAGCTGAAGATGTCGACCTCGTTCTTCTTTGTACATCTACTCCAGATGATCTGTTTGGAGGTGCTGCTCAGgtatcataac ... taactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagcatggtgttttggtgttgtattcaatgttctgagctatccttaactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA
                                          ccttaac  putative branch site (score: 139)
                                      ctatcctt  CT-rich tract
                      tattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatataactgctatttatagtcttgttttctgttgattactatgagcatggtgttttggtgttgtattcaatgttctgagctatccttaactaacagGTGCTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCA

- - - - -actgcta
- - - - - - - - - - - - cttgttt
- - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - gagcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttctg