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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG

Basic information

species Zea mays
transcript GRMZM2G151863_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 3'ss of exon 7
gttagtttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctc-gacac-cttgggtttaacatttga--actctttatcctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG
                               ||  |  |  |  | | |||        || | || |  |||  | |  |  ||||| ||| |   |  ||| | |  | | |||   ||    ||||||||| |||||||||||||||||||||||||||||||| ||||||||||| || || |||
-----------------------------gaatattagttctcttttggtaagtagttatctataatatgctttttctgatgagacactctttgaaattgcatctcataatttttttctcttcccgcagGCTTTTATCTTAACCTTCTTAGCTGAATGGGGCGACCGAAGCCAAATAGCAACTATTGCG

upper sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 8
gttagtttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG
          |   ||      |  | |  |||||||| |      |||||| | |   |   |   |||||        |  | |  |||   | | |  ||   |||||     |  |||||| | ||||||||||||||  ||||||||||||| ||||| ||||| || || ||||| || 
---------gtatttttctagggcatatt-gatgctttcgg-----ttgtatgatt---tttgcggtaaactgt------ttaaaaagttgctataacccctt---ctcttgtatttttttgcagTCCTTCATCTTAACCTTTCTAGCTGAATGGGGTGACCGTAGCCAGATCGCTACAATAGCT
















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|76284808|gb|DV024376.1|DV024376
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|32801015|gb|CD953251.1|CD953251
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTA
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTA
EST: gi|71764493|gb|DR962430.1|DR962430
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATTTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|148955188|gb|EC900710.2|EC900710
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|101393554|gb|EB818709.1|EB818709
EST:     CAACCATCCGTAGGGTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|5124014|gb|AI745855.1|AI745855
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|78124080|gb|DV542464.1|DV542464
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|211094829|gb|FL156527.1|FL156527
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCCCTTCT-AGCTGAATGGGGCGACCGGAGCCCAATAG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACC--TTCTTAGCTGAATGGGGCGACCGGAGCCAAATAG
EST: gi|71433454|gb|DR814504.1|DR814504
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|93014798|gb|EB640318.1|EB640318
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGC
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGC
EST: gi|74242668|gb|DT650582.1|DT650582
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|71775510|gb|DR973388.1|DR973388
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|91875142|gb|EB405099.1|EB405099
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGGCCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|71757648|gb|DR955585.1|DR955585
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACGGGAGCCAA-TAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|14243778|gb|BG841491.2|BG841491
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|71417678|gb|DR804170.1|DR804170
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|78073959|gb|DV502393.1|DV502393
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCCTCTTAGCTGAATGAGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|37380324|gb|CF626963.1|CF626963
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|76291625|gb|DV031193.1|DV031193
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|16925694|gb|BM078762.1|BM078762
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|78119848|gb|DV538232.1|DV538232
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|78119849|gb|DV538233.1|DV538233
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|67010532|gb|CO439281.1|CO439281
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTNTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|91048229|gb|EB158647.1|EB158647
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|71770354|gb|DR968291.1|DR968291
EST:     CAACCATCCGTAAGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTTACCTTTCT-AGCTGAATGGGGCGACCGGAGCCAAATAGC
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTT-CTTAGCTGAATGGGGCGACCGGAGCCAAATAGC
EST: gi|40335107|gb|CK369177.1|CK369177
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|71417675|gb|DR804169.1|DR804169
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|86466280|gb|DY232651.1|DY232651
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|91875143|gb|EB405100.1|EB405100
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GTTTTCATCTTAACCTTCTTAGCT
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCT
EST: gi|74242876|gb|DT650790.1|DT650790
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG

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: 48 (upstream exon), 47 (downstream exon)
Score: 117

GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 86

GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 85

GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG
                      gtttaac  putative branch site (score: 144)
                                    ctctttatcct  putative PPT
                       tttaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCGACAATCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA