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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagttcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC

Basic information

species Zea mays
transcript GRMZM2G109383_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
gtaatgagt--tcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC---
|||||  ||  ||||||||  |||||| | |  |  || ||| | | | ||| || |||| | |||| ||||||| ||||| ||||||||||| || ||||| ||||||||||| ||||||||||||||  | ||||| || ||||| ||||||||   ||||||||||| ||| || |   
gtaatttgttttcttctatcatcacaatt-tgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAA---ATCCTCAAATGCTGAACCCCCAG

upper sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------------gtaatgagttcttctattgtcacaaatatctactta-taatgtggctaggtattaatt-catcacttatatt------tttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGG--AAAGTCATCCT-CAAATGTTGAGCCTC
                                          ||     | ||   |   | | |||||     | |  | |||   |    ||| ||  || |||    ||       | | ||||||||||||||||| || || |||||||| || ||||||||||| || ||| | || | |||||||||  |  |  ||| | ||  | |   ||  ||||   
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC---

upper sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------gtaat-gagttcttctattgtcacaaatatctacttata-atgt---ggctaggtattaattcatcacttatatttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC
              |||   ||     |||||  || ||||   |||  ||| |  |   ||||   |||| |  ||  |   |    ||||||||||||||||||||| || ||||||||||| ||  | |||||||| || ||| | || | ||| |||||  | || || ||   | |    | ||| ||||
gtcttatttttgtctaaccaagaaacgctatt-ccataaatgattacaaatacacctccaggctcaatatttac-cacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC

upper sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
-----------gtaatgagttcttctat---tgtcacaaa--tatctactt--ataatgtggctaggtattaat---tcatcacttatatttttg----------------cagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC
            | |||   | ||   |   |||   |||  |||| |  |  ||||| |    |  ||  |||   |  | | || | ||||||                ||||| ||||||||||| || ||||| |||||||| || ||||||||||| |||||||||| | | |||||  | || || |||    | ||   |||||| |
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC

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|31363628|gb|CD447985.1|CD447985
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|211541124|gb|FL006425.1|FL006425
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|32910896|gb|CF015708.1|CF015708
EST:     GAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: GAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|67024904|gb|CO453653.1|CO453653
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|31354675|gb|CD439032.1|CD439032
EST:     GAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGCCTTCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: GAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|67022599|gb|CO451348.1|CO451348
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|67041650|gb|CO467905.1|CO467905
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAAGACTTTGGANGTGGTCATCCGGATCCTAAC-TTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|60351436|gb|DN218409.1|DN218409
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTAT
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTAT
EST: gi|67018536|gb|CO447285.1|CO447285
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|67025909|gb|CO454658.1|CO454658
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG

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: 278

TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 392

TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 773

TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... atttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatatctacttataatgtggctaggtattaattcatcacttatatttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC
                           tattaat  putative branch site (score: 773)
                                            tattttt  putative PPT
                           tattaattcatcactt  TA-rich tract