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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggttactgaatttttctggtacagacatcctcaagtactctctctgatttatagcgtttgtcattttttattccttaacgcccaaagctggaagctctggcttatgatttacctttctttgtgcttcatgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG

Basic information

species Zea mays
transcript GRMZM2G161566_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161566_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 5
gtaatggttactgaatttttctggtacagacatcctcaagtactctctctgatttatagcgtttgtcattttttattccttaacgcccaaagctggaagctctggcttatgatttacctttctttgtgcttcatgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG
        || |   ||||||||   |   | ||  | |  |   |||   || | |||| |||||    || || |  | |      ||| |||  |   |||  ||||  |||  || |   | |  || |||| || |||||||| |||||||||||| ||||||| |||   |||||||||||||| || |||||||||||||| |||||||||||||||||
-------gtaatctttttttctgaatccatcttctgctaacatgatctactatct-tagcatttgtttacttgtagttatcagaaggaaaatctgaga---ctga-ttat--tttctctgtggctctcttttatgcattacagAGTAGTGTCTTGAGGGATTTGTCCTCAATGAAGCGATTAGTTGTTGCTACTGGAGGTGGTGCTGTTATCCGACCAGTTAACTG
















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|5343250|gb|AI795555.1|AI795555
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|24934599|gb|CA452817.1|CA452817
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|37392587|gb|CF633545.1|CF633545
EST:     ATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: ATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|30087805|gb|CB886011.1|CB886011
EST:     CTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCNCC
genomic: CTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|32164833|gb|CD670151.1|CD670151
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|13237004|gb|BG355018.1|BG355018
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|60395600|gb|DN228470.1|DN228470
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|211307747|gb|FL198214.1|FL198214
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|37398941|gb|CF636791.1|CF636791
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|24934498|gb|CA452716.1|CA452716
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|32928190|gb|CF033002.1|CF033002
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|44900819|gb|CK827364.1|CK827364
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC

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: 48 (upstream exon), 48 (downstream exon)
Score: 76

TATGTTTTACAGTGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 516

TATGTTTTACAGTGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 509

TATGTTTTACAGTGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

TATGTTTTACAGTGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagctggaagctctggcttatgatttacctttctttgtgcttcatgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG
                  ttatgattta  TA-rich tract