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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctctagcgatcttgagcaaaacttgggtggtgtaaggtctatggctgtgcaaattgtgatttctgatgtgatattgtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG

Basic information

species Zea mays
transcript GRMZM2G009845_T03
intron # 3
splice site 3'
intron type U2

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|211137300|gb|FL464598.1|FL464598
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|211142696|gb|FL475568.1|FL475568
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|4775859|gb|AI664864.1|AI664864
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|78026507|gb|DV494894.1|DV494894
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|60357859|gb|DN224832.1|DN224832
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|67011792|gb|CO440541.1|CO440541
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|488236|gb|T18817.1|T18817
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTNGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGT
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGT
EST: gi|60398457|gb|DN231273.1|DN231273
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|211137299|gb|FL464597.1|FL464597
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|71322677|gb|DR798010.1|DR798010
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|211134458|gb|FL464549.1|FL464549
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|12969842|gb|BG266684.1|BG266684
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCCTTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|113701056|gb|EE678560.1|EE678560
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|78026876|gb|DV495263.1|DV495263
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|37381222|gb|CF627483.1|CF627483
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|84969435|gb|DW467872.1|DW467872
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|14245548|gb|BG874130.1|BG874130
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|37377257|gb|CF625217.1|CF625217
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|60340999|gb|DN207972.1|DN207972
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|166673354|gb|EG308254.1|EG308254
EST:     AACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: AACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
EST: gi|211175883|gb|FL475297.1|FL475297
EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

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: 327

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 393

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 484

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 313

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaggtctatggctgtgcaaattgtgatttctgatgtgatattgtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG
                              ttctgat  putative branch site (score: 313)
                                        atattgta  TA-rich tract