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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttaagttcttatgtttcactaaaattacctttctttttcttgcctgccatgtaatgaccagttaatctcaataatactatttttttattattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG

Basic information

species Zea mays
transcript GRMZM2G175071_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16350.1 (Oryza sativa), 3'ss of exon 3
cttcttaagttcttatgtttcactaaaattacctttctttttcttgcctgccatgtaatgaccagttaatctcaataatactatttttttattattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG
 || |||   |||  | |||  |     |   | ||  |||  || ||   ||  |  | |||  | | | ||   |  | |  || ||| | ||||||| |||||||||| |||||||| ||||| | ||| |||| ||| |  |||||| |  ||||||||||||| ||||||||||||
tttattataatctattttttatcctgtttgttcattggtttatttacccatcacatctttaccgttgagtttctcaataatttcttgtttctaattgtagCTAGCTGATGCTAAGGATGTGATGGATGTAGTCCGGAATATTGAAGGTGTAAGCCTTCCTGTATTGACACCAAACCTTAAG

upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 3
cttcttaagttcttatgtttcactaaaattacctttctttt---tcttgcctgc-catgtaatgaccagttaatctcaataatactatttttttattattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG
  | ||| | |  | | |||     |  ||   ||   ||    |||| |   | | || | |||   ||  ||   | | || |  | ||| | || ||  ||||||| ||||| ||||||||||||||||||||||||| | ||| |||||   | || |||||  |||| || ||  | || 
--ttttatgcttatgtattttctagatgttggattctattggtgtcttacagactcttgaattgaatggt--atacaatttattccttctttatcttgttacagTTAGCAGATGCAAAGGATGTTATGGAAGCAGTTCGGAATTTGGAGGGTGCTAGATTACCTGTGCTGACACCTAATTTAAAA
















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|76293872|gb|DV033440.1|DV033440
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|211148321|gb|FL359569.1|FL359569
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAACAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|149111653|gb|EE190797.2|EE190797
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|74240108|gb|DT648022.1|DT648022
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|148975813|gb|EE025803.2|EE025803
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGG
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGG
EST: gi|60401129|gb|DN233936.1|DN233936
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATTGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|71430395|gb|DR811445.1|DR811445
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|74237799|gb|DT645713.1|DT645713
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|149010241|gb|EE042063.2|EE042063
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|148969536|gb|EE020363.2|EE020363
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|76013106|gb|DT940276.1|DT940276
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|71772253|gb|DR970190.1|DR970190
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
EST: gi|74235239|gb|DT643153.1|DT643153
EST:     TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAG                         TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA
genomic: TACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTA

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: 212

GCCAACACCTGTAAAGGTTGAGCTTATACGAAGATTGGCCACATCTGGATTACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

GCCAACACCTGTAAAGGTTGAGCTTATACGAAGATTGGCCACATCTGGATTACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 231

GCCAACACCTGTAAAGGTTGAGCTTATACGAAGATTGGCCACATCTGGATTACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 72

GCCAACACCTGTAAAGGTTGAGCTTATACGAAGATTGGCCACATCTGGATTACCTGTTGTGGAGGCAACGAGTTTTGTATCTCCAAAATGGGTACCTCAGgtatagtgct ... attattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgccatgtaatgaccagttaatctcaataatactatttttttattattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG
                  agttaat  putative branch site (score: 72)
                                      tttttttatt  putative PPT
                  agttaatctcaataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttaagttcttatgtttcactaaaattacctttctttttcttgcctgccatgtaatgaccagttaatctcaataatactatttttttattattgtagTTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG

- - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - tgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - -catgtaa