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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccactcgaccatcctattattatgaatgtttggttcactattgcccccaggagtcattgcttgagacgttccacttaagctgattgcttaatctgctcaaacacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG

Basic information

species Zea mays
transcript GRMZM2G099056_T01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 24
gttagccactcgaccatcctattattatgaatgtttggttcactattgcccccaggagtcattgcttgagacgttccacttaagctgattgct-taatctgctcaaacacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG
             | | | |   |  |  |  || ||| ||  |||    |   ||  |       ||  | |  |   | | ||||||| || | | |||||  ||   |||||||| |||||||||||||| ||||||||||| ||||||||||| || ||||| ||||| |||||||| |||||||| ||    || |||||||| |||||||
------------gcaaacatcgcaaaaaaacagtgtggatctttatgattcattggttttccaatgtggaatggcc---tcatgctgatttctgtcacctgct-gaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG
















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|6827336|gb|AW330979.1|AW330979
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|86469278|gb|DY235648.1|DY235648
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|50324254|gb|CO519380.1|CO519380
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|50324253|gb|CO519379.1|CO519379
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|12046013|gb|BF728048.1|BF728048
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|5608489|gb|AI902156.1|AI902156
EST:     AGACCCTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTGACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|5597302|gb|AI891400.1|AI891400
EST:     AGACACTTACCTCCGATGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGTTTTGTTCAGATGGTGACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|30032170|gb|CB834021.1|CB834021
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACCCGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|31405680|gb|CD484412.1|CD484412
EST:     AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACCCGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
EST: gi|30087811|gb|CB886017.1|CB886017
EST:     AGACACTGACCTCCGACGAGTTGTTTCNNNNNNNNTGGGACAAGTGCAAG                         AAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA
genomic: AGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATA

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: 177

ATTGATAAGTCAATTAGCGCCATGTACAGGAGGTTGCAAAAGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

ATTGATAAGTCAATTAGCGCCATGTACAGGAGGTTGCAAAAGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

ATTGATAAGTCAATTAGCGCCATGTACAGGAGGTTGCAAAAGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

ATTGATAAGTCAATTAGCGCCATGTACAGGAGGTTGCAAAAGACACTGACCTCCGACGAGTTGTTTCCTTCGCTGTGGGACAAGTGCAAGgttagccact ... acacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcttgagacgttccacttaagctgattgcttaatctgctcaaacacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG
                              gcttaat  putative branch site (score: 111)
                                ttaatct  TA-rich tract