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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttgtatttctgtcttcttaatgaaatgacatgcaattctcctgcctagtttgagggaaaaatccgcttctaacatttgaatattttcaatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC

Basic information

species Zea mays
transcript GRMZM2G047310_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047310_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 14
---tccttgtatttctgtcttcttaatgaa-atgacatgcaattctcctgcctagtttgagggaaaaatccgcttctaacatttgaatattttcaatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC
   | | |  |  | | |||| || |  |  ||   |||   |  | |    | ||||     | |  |    |  |||||| | |  |  | ||    | ||||| || |||||  | ||||     || || || ||||| |  ||  ||||||||||||| |||||||||||||| ||||| |  || |||||     || 
ctatgcctccacctatttctttttcaccagtatactatg-gttaattcattgttgtttacattatacgttatatgttaacatatta-cacatcca--tgtccagCCAGGAGTTGCTTTAAAGCTTGCTAAAGAAGGAACAGAAACCTCAACTTTCTGGTTTGCACTTGGAGGGAAACAAAGTTACAACAACAAAAAAGTCACTA
















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|211106295|gb|FL022813.1|FL022813
EST:     GCACATATGAGCAACAGCAGTGGGCAGCAAA-GTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
EST: gi|213188773|gb|FM187672.1|FM187672
EST:     GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
EST: gi|211106299|gb|FL022817.1|FL022817
EST:     GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAG                         CCTGGCATTGCAGTGAAGCACTGCAAGGAGGGGGACAGAGAGTTCTGCTTT
genomic: GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGG-ACAGAGAGTTCTGCTTT
EST: gi|211541601|gb|FL022804.1|FL022804
EST:     GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
EST: gi|211106296|gb|FL022814.1|FL022814
EST:     GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
EST: gi|211541598|gb|FL022801.1|FL022801
EST:     GCACATATGAGCAACAGCAGTGGGCAGCAAA-GTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: GCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
EST: gi|71439549|gb|DR820599.1|DR820599
EST:     ACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: ACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
EST: gi|5816386|gb|AI987302.1|AI987302
EST:     ATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAG                         CCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC
genomic: ATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTC

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: 891

TTTCGTACTGCAATCTGGAAATGCTATGTTTACATGGTTTGGCAATTCTAGCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 617

TTTCGTACTGCAATCTGGAAATGCTATGTTTACATGGTTTGGCAATTCTAGCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 518

TTTCGTACTGCAATCTGGAAATGCTATGTTTACATGGTTTGGCAATTCTAGCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1104

TTTCGTACTGCAATCTGGAAATGCTATGTTTACATGGTTTGGCAATTCTAGCACATATGAGCAACAGCAGTGGGCAGCAAAAGTTGCTGAATTTTTGAAGgtatgagggc ... aatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctagtttgagggaaaaatccgcttctaacatttgaatattttcaatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC
                        ttctaac  putative branch site (score: 1104)
                           taacatttgaatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttgtatttctgtcttcttaatgaaatgacatgcaattctcctgcctagtttgagggaaaaatccgcttctaacatttgaatattttcaatcttacagCCTGGCGTTGCAGTGAAGCACTGCAAGGAGGGGACAGAGAGTTCTGCTTTCTGGTTTGCTCTTGGAGGGAAACAGAGTTATACAAATAAAAACACTCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC