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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttcggccacctgcttcctacctccccgctcctcccctcagatccgcatcgagctacccgttagagctctgcccgagctgatcgtggcctctcc...

Basic information

species Zea mays
transcript GRMZM2G174644_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 1
ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGC------TTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttcggccacctgcttcctacct-ccccgctcctcccctcagatccgcatcg----agctacccgttagagctctgcccgagctgatcgtggcctctcc
         | || || || || ||||||||||||      |||||||| ||| ||||||||||| ||||||||| |||||||||||| || ||||| |||||||||||||| |||  |||||  | ||   ||   | | |   | |   ||   |||   |     || | ||     ||||||  |||||  || ||    || |   
------GGAGTGGAGCCGCCTCGTCGGGAGGCGGCGGGGGCTTCTTCTCCTCGATCGCCGCCGGCGTGCGCAGCTTGGGCACCGCCGTCCACAAATCTGTCAACGGgtgagtcttcc-ccacccccctcgcgccggtctctcagttgcttgcaaccccgtgccctctcagatcccgacctgagctcc-cccgatttgttcacccccac---
















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|13150716|gb|BG321038.1|BG321038
EST:     CCGCCGGCATGCGCA-CTGGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: CCGCCGGCATGCGCAGCTGGGG-CACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211272002|gb|FK970185.1|FK970185
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211272000|gb|FK970183.1|FK970183
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271996|gb|FK970179.1|FK970179
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271999|gb|FK970182.1|FK970182
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271997|gb|FK970180.1|FK970180
EST:     GCCGCCGGCATGCGCM--TGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTNAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271998|gb|FK970181.1|FK970181
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211272003|gb|FK970186.1|FK970186
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|149009147|gb|EE041283.2|EE041283
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|18659308|gb|BM500269.1|BM500269
EST:     GCCGCCGGCATGCGCAN-TGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA

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: 222

ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 475

ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 407

ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 233

ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttcggccacctgcttcctacctccccgctcctcccctcagatccgcatcgagctacccgttagagctctgcccgagctgatcgtggcctctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc