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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtcccatcattctgatctcatttgtatgaggatttttgtcctcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 3
--gttgtcccatcattct----gatctcatt-tgtatgaggatttttgtcctcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA
  | |   |  | ||| |    ||    ||  | ||||  ||| || | |     ||||||||||||| || |  | |  ||  |  | |  | ||   || ||||||||||||| |||| || |||||||||||||||||||| ||||||||||| ||||||||||||||| |||| || || ||||| ||||||||||| ||||
cggctccgcatttattttctatgactatatcctatatggagatcttcgac-----ttcttttttgtttctgtttgt-taattattgaagtacgcttgcattgacagATTGTTCGGCTTCTGGCAAACCACCCTCAGTTTCATATCAAAGTGATGACCGCAGATAGAAAAGCTAGCGAACAGTTCGGATCTGTATTTCCTCATTTGA

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 3
------------------------------gttgtcccatcattctgatctcatttgtatgaggatttttgtcctcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA
                                     | |   | || || |||||   ||| ||||| | |||||     |||  |    |||||||||||||      | |   |||   ||  ||||||||  || ||||||| ||||| ||||| |||| ||| |||||||||||||||||||||||||||||||| || |||||||| |||||||||||||| |
gttgctacactctttctcctattccggctcaccacttctttgatatggtcccatttcattgaagatttctatcctc-----tttggttcgattgctaatgtgttca----aatacatttgcattggcagATTGTCAGGCTTCTAGCAAACCATCCTCAATTTCGTATCAAAGTGATGACTGCAGATAGAAAAGCTGGCGAACAGTTTGGATCTGTATTTCCTCACTTAA
















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|78093374|gb|DV521748.1|DV521748
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|31354246|gb|CD438603.1|CD438603
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345290|gb|FL126063.1|FL126063
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345286|gb|FL126059.1|FL126059
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345287|gb|FL126060.1|FL126060
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCASCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|148943028|gb|EC888078.2|EC888078
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|148946776|gb|EC892045.2|EC892045
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345285|gb|FL126058.1|FL126058
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|89757643|gb|DY687157.1|DY687157
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|71429367|gb|DR810417.1|DR810417
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|30705270|gb|CD058727.1|CD058727
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|91878697|gb|EB408654.1|EB408654
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345293|gb|FL126066.1|FL126066
EST:     AT-CCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|78080160|gb|DV508572.1|DV508572
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|78079274|gb|DV507686.1|DV507686
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|74234671|gb|DT642585.1|DT642585
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|149074521|gb|EE162917.2|EE162917
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT

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), 46 (downstream exon)
Score: 184

TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 135

TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 101

TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA
                  tgctaat  putative branch site (score: 101)
                                          tttttgtt  putative PPT
     tcttttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtcccatcattctgatctcatttgtatgaggatttttgtcctcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG