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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcccctatttttctttccttcagttctgcaatgttttttttcctcaggttactagggacacggctcaccatgaacaccacttgcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT

Basic information

species Zea mays
transcript GRMZM2G304362_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 16
gtattgcccctatttttctttccttcagttctgca-atgttttttttcctcaggttactagggacacggctcaccatgaacaccacttgcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT
                | | || |   |  || |  ||  || |||| |     || ||    |  |  |||||||| || |  | |||  || | |     ||          | | ||| || ||||| || ||||||||||| || ||||| ||||| |||||||||||||| |||||| ||||||||||||   
---------------gtatgtcttctggccctccccataattgttttac----attcctgaatagccaactcaccattaaaaata-ttgttcagGAAAAC-GGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA---
















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|16926106|gb|BM079174.1|BM079174
EST:     GAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: GAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|24769909|gb|CA405038.1|CA405038
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|76016674|gb|DT943844.1|DT943844
EST:     CAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|5762221|gb|AI967269.1|AI967269
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|6827647|gb|AW331290.1|AW331290
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|5714044|gb|AI944029.1|AI944029
EST:     CGATCAAGTTCCCAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCCCAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|13150171|gb|BG320493.1|BG320493
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|60672569|gb|DN475271.1|DN475271
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|32907431|gb|CF012244.1|CF012244
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|211402195|gb|FL458654.1|FL458654
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|6022688|gb|AW067616.1|AW067616
EST:     CGATCAAGTTCACAGGGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|31356810|gb|CD441167.1|CD441167
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|32938836|gb|CF043655.1|CF043655
EST:     CGATCAAGTTCACAGTGGATACCACACTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|32944077|gb|CF048896.1|CF048896
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|91053675|gb|EB164093.1|EB164093
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|211165342|gb|FL103230.1|FL103230
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGCAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|7227815|gb|AW566456.1|AW566456
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|5081116|gb|AI738162.1|AI738162
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|29545140|gb|CB605318.1|CB605318
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|4646500|gb|AI491639.2|AI491639
EST:     CGATCAAGTTCACAGTGGATACCNCGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|31405947|gb|CD484679.1|CD484679
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|32932471|gb|CF037283.1|CF037283
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|32938437|gb|CF043256.1|CF043256
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|6102094|gb|AW126564.1|AW126564
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|211402194|gb|FL458653.1|FL458653
EST:     CGATCAAGTTCACAGTGGATACCACGCTTYTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|28982344|gb|BQ538349.2|BQ538349
EST:     GAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: GAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|60343761|gb|DN210734.1|DN210734
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|32944136|gb|CF048955.1|CF048955
EST:     CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
EST: gi|5739621|gb|AI947416.1|AI947416
EST:     CGATCAAGTTCCCAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGG                         GTTAGCGATGAAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG
genomic: CGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAG

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: 416

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCGATCAAGTTCACAGTGGATACCACGCTTCTGAAGGAGAATGGGAACGGGgtattgcccc ... gcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctcaggttactagggacacggctcaccatgaacaccacttgcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT
                        ggctcac  putative branch site (score: 79)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcccctatttttctttccttcagttctgcaatgttttttttcctcaggttactagggacacggctcaccatgaacaccacttgcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG