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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcag

Basic information

species Zea mays
transcript GRMZM2G161969_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 16
GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcg--tgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcag
|||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| |||||| || || ||||||||||| | |||||||||||||||| |   ||||  ||| |    |||||| ||          || || |  |    |  |  |   ||   |   |||||||
GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGGTGGCTCAAAGAGCAAGGGATAACAGCTTAAAACCTGAAGATTATGAGgtatatggatcgcatggtagctaatataagcatga----------gacaacatcatttttccttgaaaattctggtgcttttcag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 16
GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcg--tgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcag
|||||||||||||| ||||||||||  ||||| ||||||||||||||||||||||||| |||||| || || || || |||||||  ||||||||||||||| |  || ||  ||| |    |  ||| |||| || |        |     |||||| |  || |   ||   |||||||
GATGCAGACAAGAAAGGACTTGGTATGATTGCGGAGGAGGTGAAGCAGTTGGCTCAAAGAGCAAGGGATAACAGTTTGAAACCAGATGATTATGAGgtatatggattgtatggtagttaatttttgcatgaaacaacagc------atttttccatgagaacttttatgtggtgttttcag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 5'ss of exon 16
GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtgcatactaggtgtgctaagcaggaaaga-agaaatgagaaaaaaaaccatgatatattgttgctgcatttttcag
|| ||||||| |||||| ||    |||||||  || || ||   |   || ||||||||||||| ||| || |||||||| |||| ||||||||||||     | |   | |   | |  ||  ||  ||  | |    | || ||| |  | |  | || | |||    ||        
GACGCAGACAGGAAGGGTCTGTCCACAATTGGAGAAGAAGTTCGGTTATTAGCTCAAAAAGCAAAAGAGAACAGCTTAAAGCCAGAAGATTATGAGgt-----gagagaattcattatcttactcactaatcatatctttcagtaaacatgctaata-atctcgttttctcag-------

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|71329666|gb|DR801555.1|DR801555
EST:     AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG                         GGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
EST: gi|21809699|gb|BQ668017.1|BQ668017
EST:     AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG                         GGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
EST: gi|5439400|gb|AI820321.1|AI820321
EST:     AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG                         GGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
EST: gi|32930403|gb|CF035215.1|CF035215
EST:     AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG                         GGTGGCACCTTCACGGTATCAAACATGGGAGGTCCCTTCGGAATCAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG                         GGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
EST: gi|148935652|gb|EC879696.2|EC879696
EST:     AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG                         GGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
EST: gi|4776441|gb|AI665444.1|AI665444
EST:     GCTTAAAACCAGCAGATTATGAG                         GGTGGC-CTTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA
genomic: GCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAA

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: 158

GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 395

GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtg ... catttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAGgtatatcgtgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT