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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgcctgcacagcgtcttgaacgatctgtgctcaagttcttcgttctgatgtgctgctccatctttttttttttaccttgcag

Basic information

species Zea mays
transcript GRMZM5G840928_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T04 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 5'ss of exon 10
TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgcctgcacagcgtcttgaacgatctgtgctcaagttcttcgttctgatgtgctgctccatctttttttttttaccttgcag
| |||| ||| || |||||  |||||||||| ||||||||||||||||||||||||||||| ||||||||| |||| |||||||||||  ||||||||||||| | ||||   | ||     ||    | |     ||    |  |   |  | || |  |  | || |||    ||||   |||||||
TTGCTGGCTCTCTACTACTTAGGAAAGCTGCATCACATGCTTTTGAGAAGAACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgcgctctcactagattttttgtttca-acttgtatcgtatttcttcatttttt-ttacaccttgcacttttcctcttgcag
















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|71763117|gb|DR961054.1|DR961054
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATTTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|76282803|gb|DV022371.1|DV022371
EST:     AACAAGAGATCGACTGTCACCTTTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATTTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|76018445|gb|DT945615.1|DT945615
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|76016157|gb|DT943327.1|DT943327
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|211044162|gb|FL460073.1|FL460073
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|94474415|gb|EB703373.1|EB703373
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATTTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     AACAAGAGATCGACTGTCACCTTTGATATCATTGAGTTTTTGGGCAAAAG                         CTTGGAAGATATTTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|211044163|gb|FL460074.1|FL460074
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|32933908|gb|CF038720.1|CF038720
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTGGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|60345505|gb|DN212478.1|DN212478
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|89249188|gb|DY620974.1|DY620974
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|4680975|gb|AI629645.1|AI629645
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
EST: gi|50323071|gb|CO518197.1|CO518197
EST:     AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAG                         CTTGGAAGATATTTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT
genomic: AACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGT

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: 145

TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGTCATGCACGCGGAAGCCTAATAATGTTTATATGTCTGTTGAACAGGGTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGTCATGCACGCGGAAGCCTAATAATGTTTATATGTCTGTTGAACAGGGTGT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 26

TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGTCATGCACGCGGAAGCCTAATAATGTTTATATGTCTGTTGAACAGGGTGT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 38

TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgc ... taccttgcagCTTGGAAGATATCTGCCCTGCCGAGCACTAGCTCCTGCCAGTAATTGTAGTCATGCACGCGGAAGCCTAATAATGTTTATATGTCTGTTGAACAGGGTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCTGATATCATTGAGTTCTTGGGCAAAAGgtctgtgtgcctgcacagcgtcttgaacgatctgtgctcaagttcttcgttctgatgtgctgctccatctttttttttttaccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC