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

gtgagatctgtttcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctttacataccataggtaaaaattttgtgtggtagattgttactaaattgctcaatttttctattcatcaatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTGATGACTAATGACACGACTGACAATAATCCTGAAGAAGCTGTTCACTGCT

Basic information

species Zea mays
transcript GRMZM2G030422_T03
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 19
gtgagatctgtttcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctttacataccataggtaaaaattttgtgtggtagattgttactaaattgctcaatttttctattcatcaatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTGATGACTAATGACACGACTGACAATAATCCTGAAGAAGCTGTTCACTGCT---
|| | |||||  |  | |   || ||| || |||  |  |  |   |     |||| | |     |  | |||  || ||  | ||||||     |||||||||||| ||  | |  ||| ||||| |    |||| ||||| || |||||||| |||||     |||||||||| ||||| |||||| | |||||||||||||  ||||||||    |||||||||||||| || ||||   
gttaaatctggattatttacgcacataaatatgctcagtt--ttacctacctgctc-tgtataccaggt-ccaggggcaagcaatttgtgcatatgattgttactaactt-tttatgtttgctattgac---tcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAAC---CCTGAAGAAGCTGTCCATTGCTTTG
















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|87156341|gb|DY401130.1|DY401130
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
EST: gi|19058885|gb|BM737552.1|BM737552
EST:     CTGGTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
EST: gi|19058659|gb|BM737326.1|BM737326
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAA
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAA
EST: gi|22520900|gb|BU079711.1|BU079711
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAA
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAA
EST: gi|31360482|gb|CD444839.1|CD444839
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACACTATGGCAACCACCAAGTGGCATCTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
EST: gi|22473365|gb|BU037845.1|BU037845
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG
EST: gi|6095542|gb|AW120209.1|AW120209
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAACCGCAAGTGTATCTCCCACACTATGGCAACCACCAAGTGGCATCTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatctg ... aatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtggtagattgttactaaattgctcaatttttctattcatcaatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTGATGACTAATGACACGACTGACAATAATCCTGAAGAAGCTGTTCACTGCT
                tactaaa  putative branch site (score: 1)
                             aatttttctattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatctgtttcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctttacataccataggtaaaaattttgtgtggtagattgttactaaattgctcaatttttctattcatcaatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTGATGACTAATGACACGACTGACAATAATCCTGAAGAAGCTGTTCACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT