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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 14
gtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG
||||| ||||| || ||| | |||||||          ||  ||||| | |||  ||   ||   || ||  |||  ||                               ||   || |||||||||| || ||||| |||||||| || || | ||||||||| || ||||| ||||||||||| |||||||||||| |||| || |||||||||   | 
gtttgtatctcctgttttcttcatcaca--------cggatattttccaacttcggacgaactgaattgaacaaagtct-------------------------------acctgttcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA

upper sequence: GRMZM2G059671_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 13
gtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatc-cttaagttctctcttttttgttaaaaa-atacg-tacaattttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG
                         |  | | || ||   | |  ||||    |  ||  |  ||    ||    |  ||  |||  |  | | |   | ||| | ||| | ||  |      |||||||| || ||||| |||| |||||||||| ||||||||||||| |||      ||  |||   |||| ||     | || ||| |||||||||  | 
-------------------------atggaagca-atgtgcatactctaa---tgaatgcattcctgcaagtggcttactctagtgttgacatatgactcaaatacatatgataggacggcttttgcagGTTGTAGCAGCTGTTGCTTTCAAGGGAAAAAGGCTTGAGATTCCAGCTGAAGTAAATCATCAAGTCGCCTACTTGATTGAGGCCTGCTGGGCTAA
















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|20802940|gb|BQ293990.1|BQ293990
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGT
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGT
EST: gi|19770366|gb|BQ035087.1|BQ035087
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|19822326|gb|BQ048350.1|BQ048350
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|26456039|gb|CA827622.1|CA827622
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|113703759|gb|EE681263.1|EE681263
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|88757722|gb|DY541863.1|DY541863
EST:     GGGAGCTTATGACATTGCAGCACCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|78110653|gb|DV529058.1|DV529058
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|148945985|gb|EC891279.2|EC891279
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|211160526|gb|FL223272.1|FL223272
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|19770367|gb|BQ035088.1|BQ035088
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|78544160|gb|DV621658.1|DV621658
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|19770019|gb|BQ034740.1|BQ034740
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGGCAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC

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), 49 (downstream exon)
Score: 52

CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 76

CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG
                                           ttttactt  CT-rich tract
                   ttttttgttaaaaaat  TA-rich tract