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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctatattgtttttttcagaacgttaacacaataatttggatgtagctaataacatgatctgatgtgttttttgtgttag

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 5
GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctatattgtttt----tttcagaacgttaacacaataatttggatgtagc-taataacatgatctgatgtg--ttttttgtgttag
|||||||||||||||| ||||| |||| ||||||||||| |||||| ||||| ||||||| ||| ||||| ||||||||||||||||||||| |   | |||  |     |   | ||| ||     |  |  |||  | |  | | ||||||| || |||| |   ||| || | ||||
GTTTTGTTGGGGAGACGGACAAAAACAATGAAAACAAGCGTTATCTCTACACACACAAGAGCATTCTTGTCAAATACAATGATAACAGGgtacga-gttttgcataaaagtgataaaacttttcattaccacattgcttttgacatgataacataatttgatctcattttattattttag
















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|67012575|gb|CO441324.1|CO441324
EST:     CTTGTTATTATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: CTTGTTA-AATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|60351142|gb|DN218115.1|DN218115
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|160481321|gb|EY254485.1|EY254485
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|78079180|gb|DV507592.1|DV507592
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGA-GAAGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|31356502|gb|CD440859.1|CD440859
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|71766500|gb|DR964437.1|DR964437
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|89249564|gb|DY621350.1|DY621350
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|13516079|gb|BG518355.1|BG518355
EST:     GAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: GAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
EST: gi|160481319|gb|EY254483.1|EY254483
EST:     ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG                         ATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT
genomic: ATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGT

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: 232

GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGTAAGAAATTGGAAATGACATATTCAGTGAAGTGGGTAGCGACTGATGTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 189

GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGTAAGAAATTGGAAATGACATATTCAGTGAAGTGGGTAGCGACTGATGTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 248

GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGTAAGAAATTGGAAATGACATATTCAGTGAAGTGGGTAGCGACTGATGTGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 302

GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctata ... tttgtgttagATAATTCATGTAAATCTCACCCAAGAGTCTCCTACGCTTCTTGAAGATGGTAAGAAATTGGAAATGACATATTCAGTGAAGTGGGTAGCGACTGATGTGT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGGgtatgctatattgtttttttcagaacgttaacacaataatttggatgtagctaataacatgatctgatgtgttttttgtgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC