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

gtttgttattacgtgaagctattttcacttgtggaaattttctattacaatatcatttgtgttgattgtgcttggtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 11
gtttgttattacgtgaagctattttcacttgtggaaattttctattacaatatcatttgtgttgattgtgcttggtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG
||||||||| || |||   |  | |||       ||||| | |   || | |   | |||| ||||||   ||| ||||   ||| |||||||||| |||||||| ||||||||  |||||||||| |||||||||||||||||||||||||| ||||| || || ||||| || ||| |||||
gtttgttatcacctgattttgctctca-------aaattgtgtgcaactaca--gtctgtgatgattgcttttgtttttcacagGTTGGAGGTTGCTCTTTTGTTAGTGATCTTTTTAGCGTATGGTTTTAACAATGGTGGAGCAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATG
















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|22935757|gb|BU572032.1|BU572032
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|78118622|gb|DV537006.1|DV537006
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|67031292|gb|CO460041.1|CO460041
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|50322941|gb|CO518067.1|CO518067
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|22549115|gb|BU101316.1|BU101316
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|32834891|gb|CD974569.1|CD974569
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|211408045|gb|FL038492.1|FL038492
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|67040750|gb|CO467005.1|CO467005
EST:     AGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGATGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
EST: gi|32934894|gb|CF039706.1|CF039706
EST:     AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG                         GATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA
genomic: AAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAA

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: 363

TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG


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

TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGGgtttgttatt ... gtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggaaattttctattacaatatcatttgtgttgattgtgcttggtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG
                              tgttgat  putative branch site (score: 203)
                                              tttttgt  putative PPT
     aaattttctattacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttattacgtgaagctattttcacttgtggaaattttctattacaatatcatttgtgttgattgtgcttggtttttgtagGATGGAGGTTGCACTTTTGTTGGTGATCTTCCTAGCGTATGGGTTTAACAATGGTGGAGCAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG