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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccgcaacattgtcatggttttgtcgccttggatttgttctttttcccaaagaaatgtcctctgttcaaacagatctgtaactcggtttgcagattggtgcatcgattatattgttaatctggtggaatcagactcactgcaacaagatttgtcctgagcag

Basic information

species Zea mays
transcript GRMZM5G832740_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccgcaacattgtcatggttttgtcgccttggatttgttctttttcccaaagaaatgtcctctgttcaaacagatctgtaactcggtttgcagattggtgcatcgattatattgttaatctggtggaatcagactcactgcaacaagatttgtcctgagcag
|| || |||||||||||| ||||||| ||||||||||| || |||||| | ||||||| ||   |  ||| |  |     | |||          |||| | | ||||   |||   |    | |      | |||  | |   ||     ||    | |  | |  ||||   ||  | ||      || || |  | ||         |||   || |||||
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcat----atattgc---------tttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgc----ttgcccttgtattactctggaattc----aaaaccatatcccctt--------ttttcgctaagcag
















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|30031938|gb|CB833789.1|CB833789
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGNGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|149090255|gb|EE179558.2|EE179558
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|18173505|gb|BM348893.1|BM348893
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGAAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|14203013|gb|BG836690.1|BG836690
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|29544063|gb|CB604443.1|CB604443
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|32909109|gb|CF013921.1|CF013921
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGG
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGG
EST: gi|116816600|gb|EC859352.1|EC859352
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|60343936|gb|DN210909.1|DN210909
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|29544546|gb|CB604926.1|CB604926
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|30031937|gb|CB833788.1|CB833788
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|211046404|gb|FL436681.1|FL436681
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|5058748|gb|AI737224.1|AI737224
EST:     GCNCATGAGAAGGGCCAGAGATNCAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|50327958|gb|CO523084.1|CO523084
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|4966700|gb|AI691556.1|AI691556
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|149090254|gb|EE179557.2|EE179557
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|16926162|gb|BM079230.1|BM079230
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|18163201|gb|BM333040.1|BM333040
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCATGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|5847256|gb|AW000335.1|AW000335
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|78024572|gb|DV492959.1|DV492959
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|33942278|gb|CF348878.1|CF348878
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
EST: gi|5325164|gb|AI783355.1|AI783355
EST:     GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC
genomic: GCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGC

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: 180

GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGCTCACTTGGGCGGAAGCGACGCCGATGACATATAAAACACGATCCAACAA


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 63

GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGCTCACTTGGGCGGAAGCGACGCCGATGACATATAAAACACGATCCAACAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 143

GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGCTCACTTGGGCGGAAGCGACGCCGATGACATATAAAACACGATCCAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccg ... tcctgagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGGTTCCACAAGATGCTCACTTGGGCGGAAGCGACGCCGATGACATATAAAACACGATCCAACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccgcaacattgtcatggttttgtcgccttggatttgttctttttcccaaagaaatgtcctctgttcaaacagatctgtaactcggtttgcagattggtgcatcgattatattgttaatctggtggaatcagactcactgcaacaagatttgtcctgagcag

- - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA