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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT

Basic information

species Zea mays
transcript GRMZM2G114337_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT
                                |  |  ||||   |     |    |||  |  ||||  | ||        ||   | | |||        ||| ||    ||||  || ||||||| ||| || |||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||  ||||||||||| || || ||||
-------------------------------gtaagaactctcaaa---aactcttaaatgatgtttt--tcagttgtgtttacttcccagtgatttcag--gccgtta---ttgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT

upper sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT
|| ||  ||     |||||    || |  |||||| ||  | |  |   |||   ||     ||||||  |   |    |  |  | ||         | | || | ||   |  |   ||||||||  ||| ||   |||||| ||||||||||| || || || |||||||||||||| || ||||||||||| ||  | ||||  ||    || |  |   
gtcag--ttgtactgcttgcttgcgtcttccttttattacccttaa---gccttaaagtactcattttcctctaacttcatcataatct---------ctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC

upper sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT
|| ||       ||  |||||        |  ||| | |  |   |||       ||| |  | | ||||||           |    |    ||||   || |||      |  ||  ||||||||   || || |||||||||||||||||||| ||||| || ||||||||||| ||||| || |||||||| ||||  ||||||| |   ||    || |
gtcagcacattaaactttgta--------ctctttttcccataaaaccttgtgttaaaccctcctattattt-----------ccttgtttccaacatttcttcccac-tgctgctgctttcagATGATCGATCCTACTGGAATTGCAAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTT

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|78544029|gb|DV621527.1|DV621527
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|211112077|gb|FL283002.1|FL283002
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|22818980|gb|BU499070.1|BU499070
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAAACTGGTCAGTGACGCACGTAGATTG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAA-CTGGTCAGTGACGCACGTAGATTG
EST: gi|71762012|gb|DR959949.1|DR959949
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|71773585|gb|DR971483.1|DR971483
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|20802912|gb|BQ293962.1|BQ293962
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|211093538|gb|FL437518.1|FL437518
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCAACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|76284047|gb|DV023615.1|DV023615
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCCCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|60358070|gb|DN225043.1|DN225043
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|30306660|gb|CD001333.1|CD001333
EST:     TACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: TACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|20506952|gb|BQ279416.1|BQ279416
EST:     GTGGCATAACTGTTTATTCAGATGATCACTACTTGCCAACTCTCTTCAAT                         ATGGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTG
genomic: GTGGCATAACTG-CTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagAT-GGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTG
EST: gi|101389977|gb|EB816920.1|EB816920
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|26456599|gb|CA828182.1|CA828182
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|211112078|gb|FL283003.1|FL283003
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACCCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
EST: gi|20336928|gb|BQ172558.1|BQ172558
EST:     AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT                         ATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG
genomic: AGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGG

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), 46 (downstream exon)
Score: 108

CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 68

CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 27

CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAATgtaagtgttc ... gtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT
     aaaaaaaaa  TA-rich tract