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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcatcacccaaagcataaacacttctgttgcccatatacagttctttctttctgactcttgtacatcttaaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG

Basic information

species Zea mays
transcript GRMZM2G037342_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 4
gtaagttcatc-----acccaaagcataaacacttctgttgcccatatacagttctttctttctgactcttgtacatcttaaat---ttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG
|| ||||| |      ||| || || ||| || |||  ||||     |   ||||| | |||     | ||   ||| | || |   ||||||||||||||||||||||||||| |||||||| || |||||||||||||| || | ||||||||| ||||| |||||||||||||| || || || |||||
gtcagttcttatatgaacctaatgcgtaagcatttcgattgcatgcctgtggttctgtgttttgacttgttccgcatgtgaacttttttcagCACTTGGGGCAATATTCTCGGCAACAGACTCTGTATGCACCTTGCAGGTTTTGAACCAAGATGAAACACCCTTCTTGTACAGCCTGGTTTTCGGGGAAGG

upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttcatcacccaaagcataaacacttctgttgcccatatac--agttctttctttctgactcttgtacatcttaaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG
       | | |  ||||| | |  |  |||   | |  ||  |   |||    |  |  | |    |||||   | |  || ||||  |||| ||||||||||| || |||||||| ||||||||||||||                                                      
---gtaccctgaaacaaagaaaacccttttcaagttcttattcattaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA-----------------------------------------------------
















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|148996402|gb|EE035697.2|EE035697
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|78119306|gb|DV537690.1|DV537690
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|71315380|gb|DR794294.1|DR794294
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|76921052|gb|DV168433.1|DV168433
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGGGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|32866161|gb|CF005843.1|CF005843
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         TTTTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|20300970|gb|BQ163913.1|BQ163913
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|71426858|gb|DR807908.1|DR807908
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|18964389|gb|BM660977.1|BM660977
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|50328971|gb|CO524097.1|CO524097
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|149058822|gb|EE156843.2|EE156843
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|76912611|gb|DV164818.1|DV164818
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|149015463|gb|EE045330.2|EE045330
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGT
EST: gi|148931601|gb|EC874712.2|EC874712
EST:     ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG                         CCCTTGGGGCAATATTCTCGTCCACAGACTC
genomic: ACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTC

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: 463

GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 186

GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 203

GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 294

GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTGgtaagttcat ... taaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgcccatatacagttctttctttctgactcttgtacatcttaaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG
                          ttctgac  putative branch site (score: 294)
                                      tacatcttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcatcacccaaagcataaacacttctgttgcccatatacagttctttctttctgactcttgtacatcttaaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG