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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagcattggctagaccgcatccccgccaatccatataagctttattttgtttttttttttcttcagcgctgatgctaccatttgagtttgacgacggtcggtgcag

Basic information

species Zea mays
transcript GRMZM2G113267_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113267_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g01830.1 (Oryza sativa), 5'ss of exon 7
CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagcattggctagaccgcatccccgccaatccatataagctttattttgtttttttttttcttcagcgctgatgctaccatttgagtttgacgacggtcggtgcag
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CCTTCCATGCTGCATTGGATCAACAACAGAGAATCGCCAACATCAAAGAGTTCCTGAACAAGCAGACGGCTGACTCGATGTTCCTGGTGTGCACAGATAGgtaag--gcatcgat-------cacctgaagtgaagcgcatgaaatcgattctgttttca---------agcgatgat----ctgattggatttggtgggtggca-tgcag
















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|71441045|gb|DR822095.1|DR822095
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|71308808|gb|DR790647.1|DR790647
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|76920136|gb|DV168027.1|DV168027
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|71444583|gb|DR825633.1|DR825633
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|149111889|gb|EE191046.2|EE191046
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|149086256|gb|EE175797.2|EE175797
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|149082649|gb|EE171854.2|EE171854
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTTTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|78026219|gb|DV494606.1|DV494606
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTTTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|31357346|gb|CD441703.1|CD441703
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|149083804|gb|EE173175.2|EE173175
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTTTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|12969960|gb|BG266744.1|BG266744
EST:     TCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGGCTTTGCGAACGTGAACCACGTGGTGCTCTTCGG
genomic: TCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|149027555|gb|EE046565.2|EE046565
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|211220791|gb|FL456553.1|FL456553
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|32840583|gb|CD980264.1|CD980264
EST:     TTTCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|110487925|gb|EE012484.1|EE012484
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|71317553|gb|DR795508.1|DR795508
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|76914390|gb|DV165509.1|DV165509
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|4753537|gb|AI657447.1|AI657447
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|76285737|gb|DV025305.1|DV025305
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|71444660|gb|DR825710.1|DR825710
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTTTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|78109607|gb|DV528023.1|DV528023
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|71444661|gb|DR825711.1|DR825711
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
EST: gi|76914388|gb|DV165508.1|DV165508
EST:     TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAG                         GGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA
genomic: TTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGA

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), 47 (downstream exon)
Score: 22

CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGACTACCCCCGCGACCCGAGCGAGTACGTGCGGCGCGTCGGGCGGACTGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGACTACCCCCGCGACCCGAGCGAGTACGTGCGGCGCGTCGGGCGGACTGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 24

CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGACTACCCCCGCGACCCGAGCGAGTACGTGCGGCGCGTCGGGCGGACTGCC


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 24

CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagca ... gtcggtgcagGGCGTCGCGGGGCATCGACTTTGCGAACGTGAACCACGTGGTGCTCTTCGACTACCCCCGCGACCCGAGCGAGTACGTGCGGCGCGTCGGGCGGACTGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCCATGCTGCGCTGGATCAGGCCCAGCGCATCGCAAACATCAAGGAGTTCCTGAACAAGCAAACGGCTGACTCCATGTTCCTTGTGTGCACAGATAGgtcagcagcattggctagaccgcatccccgccaatccatataagctttattttgtttttttttttcttcagcgctgatgctaccatttgagtttgacgacggtcggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA