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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaacacccaataatattccctctttctaagggcgttttatttgtcataagtcaaaacttctcttaactttgaccaattttgtaggaaaatatgtt...

Basic information

species Zea mays
transcript GRMZM2G119482_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 18
TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaacacccaataatattccctctttctaagg----gcgttttatttgtcataagtcaaaacttctcttaactttgaccaattttgtaggaaaatatgtt
|||||| || || || ||||||||||||||||||||||| || || ||| ||||||| || || |||| || || |||||||| || || ||||| |||||||||| || | | | || | | || | || | || || | | |||| | | || || | | |||| | |
TGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTTCGGAAGCTCTTGAATATGGACTAGTCGGTGTGAACGAGGGGATCATCTCAACAGAGgtaagaagca---agcaccgtcccagataacaaaagctaagcaactccattctccttatggtccactt-tataaatgctgttctaacttgttttttcttcag--
















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|149008263|gb|EE040415.2|EE040415
EST:     TTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTTTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|78179569|gb|DV549942.1|DV549942
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGGATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|5608478|gb|AI902055.1|AI902055
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGGATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|16916474|gb|BM072858.1|BM072858
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAG                         GTGGCGCCATTTGTCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|6827661|gb|AW331304.1|AW331304
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|76921993|gb|DV168796.1|DV168796
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|76286305|gb|DV025873.1|DV025873
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|60348461|gb|DN215434.1|DN215434
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
EST: gi|60341947|gb|DN208920.1|DN208920
EST:     CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGGATTATTTCAACGGAG                         GTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG
genomic: CTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCG

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: 47 (upstream exon), 49 (downstream exon)
Score: 306

TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCGAAGTACGGCATTGACGAGTACTTGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 606

TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCGAAGTACGGCATTGACGAGTACTTGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 309

TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCGAAGTACGGCATTGACGAGTACTTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaaca ... aaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCGAAGTACGGCATTGACGAGTACTTGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTCAACGGAGgtaagaaacacccaataatattccctctttctaagggcgttttatttgtcataagtcaaaacttctcttaactttgaccaattttgtaggaaaatatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaata