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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctctactcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG

Basic information

species Zea mays
transcript GRMZM2G146786_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctctactcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
     | |    |   |||| |  || |||  ||| ||||||||| |||||||||||||||||||||||||| |||||||| || |||||||  | ||||||||| ||||||||||||||  ||||||| |||||||| || |||||||
ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
--------------------------------------tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
                                      |  ||     ||||| ||      |  ||  | |   | | | || ||||||||||| | ||||||| |||| |  ||  | | ||||| |||| | | |||||||||||||||||||| ||  | ||||| |||||||| |||||||| |
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgag-ggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
|||| |  | |   ||||    |     |    | |   ||  || ||||||||||| | ||||||| |||| |  ||  | | ||||| |||| | | |||||||||||||||||||| ||  | ||||| |||||||| |||||||| |
tcaactttcaagcaattttttgtgcaatttgagggattttg--ctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G33570.1 (Glycine max), 3'ss of exon 2
tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
|||| |  | |   ||||    |     |    | |   ||  || ||||||||||| | ||||||| |||| |  ||  | | ||||| |||| | | |||||||||||||||||||| ||  | ||||| |||||||| |||||||| |
tcaactttcaagcaattttttgtgcaatttgagggattttg--ctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
--------------------------------------tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
                                      |  ||     ||||| ||      |  ||  | |   | | | || ||||||||||| | ||||||| |||| |  ||  | | ||||| |||| | | |||||||||||||||||||| ||  | ||||| |||||||| |||||||| |
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgag-ggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 2
tcaaatgactaagcatttccaataggtatcagtgtacaa-tgttcttataacatgccctgacagggattttggttctct---actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
     ||| |      ||  | |   |||  |    | | | |||| ||||| ||||| | |||||||   ||  |      | |   |||||  | |  | ||||||||||||||||||||||  | |||||||| ||||| |||||||| |
----gtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagggataacggccccgccacattttctggttattgcatatagATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------tcaaatgactaagcatttccaataggtatcagtgtacaa-tgttcttataacatgccctgacagggattttggttctct---actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
                                    | || ||| |      ||  | |   |||  |    | | | |||| ||||| ||||| | |||||||   ||  |      | |   |||||  | |  | ||||||||||||||||||||||  | |||||||| ||||| |||||||| |
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG

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|211273251|gb|FL384319.1|FL384319
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211532797|gb|FL373547.1|FL373547
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211082871|gb|FL417813.1|FL417813
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211536312|gb|FL400261.1|FL400261
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211413441|gb|FL400135.1|FL400135
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211334889|gb|FL419773.1|FL419773
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211385044|gb|FL404090.1|FL404090
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211421419|gb|FL412843.1|FL412843
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|32943201|gb|CF048020.1|CF048020
EST:     GATAAGATCGACGATGGGGACCATCACCTTCCAGCGCATGTTTTCTAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: GATAAGATCGACGATGAGGA-CATCACCTTCCAGCGCATGGTTGC-AAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211024425|gb|FL373964.1|FL373964
EST:     GGATAAGATNCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: GGATAAGAT-CGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211527056|gb|FL387984.1|FL387984
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211500127|gb|FL425199.1|FL425199
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211494457|gb|FL428223.1|FL428223
EST:     WGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCMAAG                         ATGCMAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211346219|gb|FL403635.1|FL403635
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGANGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|93016518|gb|EB642038.1|EB642038
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211271661|gb|FL410597.1|FL410597
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTT-CTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|211039375|gb|FL382073.1|FL382073
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|89758028|gb|DY687371.1|DY687371
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGGTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
EST: gi|33771049|gb|CF273343.1|CF273343
EST:     AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG                         ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
genomic: AGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG

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: 40 (upstream exon), 48 (downstream exon)
Score: 106

ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 73

ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAGgttagaccga ... ataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataacatgccctgacagggattttggttctctactcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
                    atttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctctactcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg