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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagctttacatttttactctgcaccaatgttttcctccaataaaatgtttcagtcattatcatcgctatgaagctgtgatgttttggtcagtttctttaaactatcagctttgctattaacaagtttcattttggcatagtcag

Basic information

species Zea mays
transcript GRMZM2G171688_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 5'ss of exon 6
GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagctttacatttttactc-tgcaccaatgttttcctccaataaaatgtttcagtcattatcatcgctatgaagctgtgatgttttggtcagtttctttaaactatcagctttgctattaacaagtttcattttggcatagtcag
|||||||| || |    ||||||||||||||| |||||||| || || ||||||||||||||||| |  ||||||||     |  || | |||  ||    |||  |||   |    |  |    |  |||  |   | |      ||| |||  ||| |  || |||  ||||||||| ||||   ||   ||||| || | ||||
GATAAAAGTGGTGTTGCACTTGAAGCACATGAAAAGTTTGCAGAGCCTAGAGAAGTGGAGgtgagatcaacatttttctaagtttacaactgtactctgttaattgaataaatagaactatgctctttctactatattat------ttgatcaccttcct-gaattatatgctttgctaataac---ttcttttttgacacattcag
















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|31356439|gb|CD440796.1|CD440796
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTAGAG                         AAATTAGTTATAACGCCATCGAAGAAAGAACTTGGGCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|60350427|gb|DN217400.1|DN217400
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAG                         AAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|20301525|gb|BQ164468.1|BQ164468
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTAGAG                         AAATTAGTTATAACGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|211259613|gb|FL189918.1|FL189918
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAG                         AAATTAGTTATAATGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|26558249|gb|CA830484.1|CA830484
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTAGAG                         AAATTAGTTATAACGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|5928612|gb|AW056009.1|AW056009
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAG                         AAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|5555434|gb|AI881385.1|AI881385
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTAGAG                         AAATTAGTTATAACGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|21987499|gb|BQ779027.1|BQ779027
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTAGAG                         AAATTAGTTATAACGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|211325873|gb|FL057941.1|FL057941
EST:     AGTTTGCTGAACCCAGAGAAGTGGAG                         AAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: AGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|213173866|gb|FM192224.1|FM192224
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAG                         AAATTAGTTATAATGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG
EST: gi|31354132|gb|CD438489.1|CD438489
EST:     GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTAGAG                         AAATTAGTTATAACGCCATCGAAGAAGGAACTTGGTCTTGCATTCAAAGGG
genomic: GCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGG

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: 128

GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGGAACCAGAAGTTGGTTGTTGAGTCATTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGGAACCAGAAGTTGGTTGTTGAGTCATTGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGGAACCAGAAGTTGGTTGTTGAGTCATTGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagcttta ... gcatagtcagAAATTAGTTATAACGCCATCAAAGAAGGAACTTGGTCTTGCATTCAAAGGGAACCAGAAGTTGGTTGTTGAGTCATTGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAAAAGCGGCGAGAAACTTGAAGCACATGAGAAGTTTGCTGAACCCAGAGAAGTGGAGgtgagctttacatttttactctgcaccaatgttttcctccaataaaatgtttcagtcattatcatcgctatgaagctgtgatgttttggtcagtttctttaaactatcagctttgctattaacaagtttcattttggcatagtcag

- - - - - - - - -  TTGAAG
- - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG