Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatctcacttgacttgttgatgagcttgtacttattaatttcaaggaagtctgcacattgtaagtgtacatataactgaacatattttcttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA

Basic information

species Zea mays
transcript GRMZM5G821611_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 2
---ttaatctcacttgacttgttgatgagcttgtacttattaatttcaaggaagtctgcacattgtaagtgtacatataactgaacatattttcttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA
    | | |    ||| |||||  || |  || |    ||  ||||| | |   | | ||  ||  || | |||| |||||| ||  | ||||| |||   ||||||||||| |||||||   ||| |||||||||||||||||||| ||||| || ||  ||||||||||||| ||||||  | ||||||||| ||| ||  
gcactgaccatggttg-cttgtc-ataattttttctgcatgtatttctaaggtttatacattttcaaaatatacaaataact-aatttgttttcattttatagGATTTGACGCTGCTTCTCCTTACTTCTGGTAGAGATCCTGGTATTATACCTCGTAACACTCATCCTCCTGAGCCTGAAGGCTTTGATGGGAGCAATGATT
















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|94472112|gb|EB701070.1|EB701070
EST:     ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTAT                         GATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
genomic: ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
EST: gi|149089592|gb|EE178843.2|EE178843
EST:     ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTAT                         GATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
genomic: ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
EST: gi|89758330|gb|DY687546.1|DY687546
EST:     CTTCACTATTTAT                         GATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
genomic: CTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
EST: gi|149087864|gb|EE177142.2|EE177142
EST:     ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTAT                         GATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
genomic: ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
EST: gi|71313270|gb|DR793166.1|DR793166
EST:     ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTAT                         GATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
genomic: ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
EST: gi|19350925|gb|BM895457.1|BM895457
EST:     ATAGCTGGGGAATCTCAGTGATGGTAGTATTGGTTGTCTTCACTATTTAT                         GATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC
genomic: ATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCC

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: 46 (upstream exon), 49 (downstream exon)
Score: 181

GGTTGTCTTCTGTCTGTTTGTTGCAAGGCATCTCATAAATGATTTCCCCGATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

GGTTGTCTTCTGTCTGTTTGTTGCAAGGCATCTCATAAATGATTTCCCCGATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

GGTTGTCTTCTGTCTGTTTGTTGCAAGGCATCTCATAAATGATTTCCCCGATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

GGTTGTCTTCTGTCTGTTTGTTGCAAGGCATCTCATAAATGATTTCCCCGATAGCTGGGGAATCTCAGTGATGGTAGTAGTGGTTGTCTTCACTATTTATgtaagcacta ... cttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaagtctgcacattgtaagtgtacatataactgaacatattttcttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA
                          atataac  putative branch site (score: 220)
                                       tattttcttttacc  putative PPT
                                   aacatattttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatctcacttgacttgttgatgagcttgtacttattaatttcaaggaagtctgcacattgtaagtgtacatataactgaacatattttcttttaccagGATTTGACGTTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCCCGGAATTCTCATCCTCCTGAACCTGAATCCATTGATGGGATCAACGACA

- - - - - - - - tgttgat
- - - - - - - - - - - -gagcttg
- - - - - - - - - - - - - - - - - - - - - - - - - gtctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgaa