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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacttctaagcttatgttctaaattcttttgtttcaaaggtcgtagtggcaatatttgaataatataaactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA

Basic information

species Zea mays
transcript GRMZM2G381744_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 12
--------------gtatgacttctaagcttatgttctaaattcttttgtttcaaaggtcgta-gtggcaatatttgaataatataaactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATA-GTTGTTTTCTTTGTATCA-----
              |||    |       |||      || |    | ||||||    ||  |  ||  |||  |||   |  || || | | |||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||       |||||||| |||||||||| |     | | | || |   | |       
gtaagagcaatcttgtactgttggctgtgttaaaaatgaagtgaaatcgtttcatcattcccatatgctaatgcttgtgca-catgaattatgcagATCATCATGGCAAAGCCAGCAGGAGGGCCAAGGAGAGATGCTCAGCCTGG------AATGGACGAAGATTAGTTTGCTACCGTGCTATATTTTCCATGTTTACCGT
















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|211324907|gb|FL462770.1|FL462770
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|32944885|gb|CF049704.1|CF049704
EST:     CCCTAAAATACTCTACCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|9824878|gb|BE574975.1|BE574975
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|33095218|gb|CF055212.1|CF055212
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGATGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|32919902|gb|CF024714.1|CF024714
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|110540574|gb|EE044494.1|EE044494
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|32919903|gb|CF024715.1|CF024715
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211389516|gb|FL138776.1|FL138776
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211389515|gb|FL138775.1|FL138775
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211335351|gb|FL444762.1|FL444762
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|60349872|gb|DN216845.1|DN216845
EST:     CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG                         ATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT

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: 153

GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 98

GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAGgtatgacttc ... aactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttttgtttcaaaggtcgtagtggcaatatttgaataatataaactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA
                                               ctctcc  CT-rich tract
                            aatatttgaataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacttctaagcttatgttctaaattcttttgtttcaaaggtcgtagtggcaatatttgaataatataaactctccagATCATTATGGCAAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGATTAGTTTGATTATAGTTGTTTTCTTTGTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT