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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttctctcagacttcttgtgtgatttaatgcagttcatatatacatatgtttgtttgtgtttgaattattggcttgatgcagaatatgattcact...

Basic information

species Zea mays
transcript GRMZM2G111713_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 5'ss of exon 11
ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttctctcagacttctt-gtgtgatt--taatgcagttca-tatatacatatgtttgtttgtgtttgaattattggcttgatgcagaatatgattcact
||||| |||||||| |||||||| || |||||||| ||||||||||| ||||| || || || ||||||||  ||| || |||  |      || |   |  |  ||   |||| | |      |    | | | ||||||  | ||| |     ||     |||| ||    
ATTGGACTCGATAAAAATGACCTTGACAAAGCTTTCATACAGCTTACGCTTGAATTCGTCACTAAACAGgtcccgtactttcattccctaaagtttagctgtttgtgtgattcaatgtggtgccactactttctttgtttgtgtcatttgtcct-tgacttttatggttt---

upper sequence: GRMZM2G111713_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv14s0030g00010.t01 (Vitis vinifera), 5'ss of exon 6
ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttctctcagacttcttgtgtgatttaatgcagttcatatatacatatgtttgtttgtgtttgaattattggcttgatgcagaatatgattcact--
||     | |||   |||||| || |||||||||| ||||||||||| ||||||||| | || || ||||| |   | ||      |  || | |  |  | |     ||| | ||    || ||| | ||  |    ||   |   ||     | | || | || |    
ATATCAATTGATCGAAATGACATGAATAAAGCTTTCATACAGCTTACGCTTGAGTTTCTGACTAAGCAGgtattaatttcc--acttggttttatcctacattttctatcaaaaatgatgatttttttatgaatcatgatcggtatattctgttacattacgcttaatcac
















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|88758132|gb|DY542273.1|DY542273
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|32845899|gb|CD985580.1|CD985580
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|76923556|gb|DV169545.1|DV169545
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|4827723|gb|AI668415.1|AI668415
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|60340408|gb|DN207381.1|DN207381
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|50337822|gb|CO532948.1|CO532948
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|89251080|gb|DY622866.1|DY622866
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|37383724|gb|CF628889.1|CF628889
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|148938687|gb|EC883023.2|EC883023
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|18181535|gb|BM382745.1|BM382745
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|89248722|gb|DY620508.1|DY620508
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|71420007|gb|DR804974.1|DR804974
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|211237149|gb|FL440871.1|FL440871
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG

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), 48 (downstream exon)
Score: 150

ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG


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

ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG


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

ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG