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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatctaacaagtataactttttcgtcttactgcctgtataaatgttactttggtctag

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 2
TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgcca-tattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatctaacaagtataactttttcgtcttactgcctgtataaatg-ttactttggtctag
|||||||| |||||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| |||||||||||||||||| || | ||  | |||||   ||||| | | ||| || | |||  |  || ||    |  |   || ||  ||| | ||||||     ||||||| || || ||||||| |||
TGTCAACCATCTGAGAACCCTGCGCATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGATTGACATAAAGTTCTTAAgtatgtcaatctttctttcattctatccttttgtttatctactatttgctctaatgccccacagattggtgta-ttttcttgtcttatgaattgtataagtgcttcctttggtttag

upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 2
TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatctaacaagtataactttttcgtcttactgcctgtataaatgttactttggtctag
|| |   |  |||  || ||| |||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || ||||| ||||||||| || |||||  |  ||  | ||||  | |  || ||||    ||      || ||    |  | ||  |   | ||||  ||   |  || |   | | |||                 
TGCCGTTCACCTGGTAATCCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAACTCATTGATAGCCAACTTGAGATAAAGTTCCTAGgtatgg-aggtttctttcat--cctatttatttc---ataagacccatcagttgacaaaactggc---tttaacagttattttataattaatttttaag----------------

upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 2
TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatctaacaagtataactttttcgtcttactgcctgtataaatgttactttggtctag
|| |  ||  |||  ||  || |||| ||||||||||||||||| |||||||||||||| |||||||| |||||||| || ||||| ||||||||| || |||||  |  ||  | ||||  | |  || ||||    ||     ||| || |  |  | ||  |    | |  |||||  | | | |   | | |||                 
TGCCGTCCACCTGGTAATACTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATTGATAGCCAACTTGAGATAAAGTTCCTAGgtatgg-aggtttctttcat--cctatttatttc---ataagacctatcagtagac-aaactggctttaacagattttt--tttaattatttttttaag----------------

upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 2
-TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctga-tctaacaagtataact-ttttcgtcttactgcctgtataaatgttactttggtctag
   || |     ||  |   || |||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| ||  ||||||||||||||  |||||||     || |  |    | |   ||   |  |      ||   ||   || |||  | |||    ||  | | |||||                                   
CCATCTAGTAG-TGCTAGTGCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATCGATAGCCAAATTGAAATAAAGTTCCAAAgtatgaaggtttctgttgtactatgtatttcatagaagagccgtcagttgacaaactggctttaatggatactattgttttcag---------------------------------

upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 2
-TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaa-agctgatc--taacaagtataacttt--ttcgtcttactgcctgtataaatgttactttggtctag
   || |     ||  |   || |||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| || |||||||| ||||||  |||||||              |||||| | |    ||||   || |||| ||||| ||||| |   |  |||  ||  ||||  | | |  || ||  |  |                    
CCATCTAGTAG-TGCTAGTGCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATCGATAGCCAACTTGAAATTAAGTTCCAAAgtatgaag----------gtttctttcgta---ctat---gtatttaatagaagagctgttggatggcaaa-atggctttaatgcatgctattgttttcag-------------------

upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatcta-acaagta-taactttttcgtcttactgcctgtataaatgttactttggtctag
|| |  || ||||  |||  |   || ||||||||||||||||| || || || |||||||||||||||||||| ||| || |||  ||||| ||| | |||| |    |   |||| ||      |  | |||| |||  |  |  ||| | || |    || |   ||| | | | | | ||   | | ||| |     | || |    |     
TGCCGCCCATCTGGAAACAATGTTCACAAATGGGGTGGTCTTGGTGAAGTTCTAGGTGGAAATGAGCTGATTGACAGTGAGATTGCGATAAAATTCATGAgtacgtttca--attcttata-----caagcttctttttcatactagtta-acagttatcgtacattcgtacttattctctagttacaataccttttctgttttttccacag-----

upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 5'ss of exon 2
TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatctaacaagtataactttttcgtcttactgcctgtataaatgttactttggtctag
||||| ||  |||  ||  |    || || |||||||| ||||| || || ||||||||||||||||| |||||||| ||  |||| || |||||   |||||||     |  ||||| ||| ||  |  ||  ||| |   || |     |   |  |    || | ||||||  |||| |    | |                          
TGTCACCCTCCTGGCAATGCAGGTCACAAGTGGGGTGGCCTTGGTGAAGTTCTGGGTGGAAATGAGCTCATTGATAGCCAAATTGATATGAAGTTTAAAAgtatg-----tacttctcctttattattcattcatatgtcaagtatggctaaggaccaac---accaatataaccatttctttgggcag--------------------------

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|60351142|gb|DN218115.1|DN218115
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|211318943|gb|FL142494.1|FL142494
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|211318946|gb|FL142497.1|FL142497
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCA
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCA
EST: gi|211318942|gb|FL142493.1|FL142493
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|160481321|gb|EY254485.1|EY254485
EST:     AATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAATGTGGAGAAGGGTTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: AATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|78079180|gb|DV507592.1|DV507592
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|31356502|gb|CD440859.1|CD440859
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|71766500|gb|DR964437.1|DR964437
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|89249564|gb|DY621350.1|DY621350
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|160481319|gb|EY254483.1|EY254483
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
EST: gi|29130633|gb|CB381337.1|CB381337
EST:     CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAA                         AAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG
genomic: CCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGG

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: 367

TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 394

TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 665

TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccata ... tttggtctagAAAACGTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAACCGTCTGAGAACCCTACACATAAATGGGGTGGTCTTGGAGAGGTCCTGGGTGGAAATGAGCTGATTGATAGTCAGCTTGAAATAAAGTTCTTAAgtatgccatattgttctcatttcttccttgtttctatttagtgtttattagaaagctgatctaacaagtataactttttcgtcttactgcctgtataaatgttactttggtctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT