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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagatttggtacctttggagaccgcctacagactttttcgtagtattgtttagatgtttatccaaatttgttcaaccatttgaatgtttctatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG

Basic information

species Zea mays
transcript GRMZM2G011068_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011068_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g44590.3 (Oryza sativa), 3'ss of exon 1
gagatttggtacctttggagaccgcctacagactttttcgtagtattgtttagatgtttatccaaatttgttcaaccatttgaatgtttctatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG
       | |||||  ||| |     |      |  |    | ||| |||| ||    | ||  |  |||||||    |||     || ||  |||||||||||| | |  | || |||||||||||||| ||||||| |||||||||||| |  |||||||| ||  ||||||| || ||||| |
----ccagatacct--ggaaaatttttgtttgttagtcttaactatggttttgagagatttcaca--ttgttca----tttcctaattcctgattatcagagataccgacagGGAAGGAGTGGCTAGCACTTCTGGACAATTCACATTCAACACATCTCTAGCCTCGTTGCACACCTATCTTGGTG

upper sequence: GRMZM2G011068_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g44590.4 (Oryza sativa), 3'ss of exon 1
gagatttggtacctttggagaccgcctacagactt---tttcgtagtattgtttagatgtttatccaaatttgt-tcaaccatttgaatgtttctatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG
    | | |  | |    |||   |    | | ||   |||  |||| ||   ||    |||     | ||    |    |||||     || ||  |||||||||||| | |  | || |||||||||||||| ||||||| |||||||||||| |  |||||||| ||  ||||||| || ||||| |
----tgtagctcatggccagatacctggaaaatttttgtttgttagtcttaactatggttttgagagatttcacattgttcatttcctaattcctgattatcagAGATACCGACAGGGAAGGAGTGGCTAGCACTTCTGGACAATTCACATTCAACACATCTCTAGCCTCGTTGCACACCTATCTTGGTG
















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|211144537|gb|FL166805.1|FL166805
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|71766061|gb|DR963998.1|DR963998
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211143112|gb|FL166799.1|FL166799
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211144535|gb|FL166803.1|FL166803
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|71448594|gb|DR829644.1|DR829644
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|71436330|gb|DR817380.1|DR817380
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|31664610|gb|CD573543.1|CD573543
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211143111|gb|FL166798.1|FL166798
EST:     GAGGAGGGTGACGGCNACGAGGAGGACTWCGACGTCGATGCCTTCCTCAG                         AGATNACWATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211144538|gb|FL166806.1|FL166806
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211144536|gb|FL166804.1|FL166804
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211144532|gb|FL166800.1|FL166800
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211144533|gb|FL166801.1|FL166801
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|211143110|gb|FL166797.1|FL166797
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
EST: gi|76288774|gb|DV028342.1|DV028342
EST:     GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAG                         AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA
genomic: GAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAA

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: 47 (upstream exon), 48 (downstream exon)
Score: 62

AGGAGCTCAACGTGGAGGTCGTCGACGACAACGAAGAAGACGAGGAGGAAGAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 32

AGGAGCTCAACGTGGAGGTCGTCGACGACAACGAAGAAGACGAGGAGGAAGAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 44

AGGAGCTCAACGTGGAGGTCGTCGACGACAACGAAGAAGACGAGGAGGAAGAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 33

AGGAGCTCAACGTGGAGGTCGTCGACGACAACGAAGAAGACGAGGAGGAAGAGGAGGGTGACGGCAACGAGGAGGACTACGACGTCGATGCCTTCCTCAGgtgattcgaa ... tatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttagatgtttatccaaatttgttcaaccatttgaatgtttctatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG
                                         tttctattt  CT-rich tract
                                     aatgtttctatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagatttggtacctttggagaccgcctacagactttttcgtagtattgtttagatgtttatccaaatttgttcaaccatttgaatgtttctatttatcagAGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG

- - - - - - - - - - - -gcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaatg