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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccagtgttcagtagtgagtactagtatatatctgtactatatatatatttgtattttgtgataattcagctgaagctgagatgatcttgtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA

Basic information

species Zea mays
transcript GRMZM2G164743_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164743_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 13
gtccagtgttcagtagtgagtactagtatatatct-gtactatatatatatttgtattttgtgataattcagctgaagctgagatga--tcttgtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA
 | | ||     ||  |   | |   || |   || ||| |   |     | || || |  | ||   || | |    ||||| |||  | ||||||| ||||||||||||||||  ||||| || |||||||||||| |||| ||  |||   |  ||||||  ||||||||||   |||||||| |||| | |||||||||
-ttctgtcggttgtcatcgatgcggatagaagactagtagtgcgttgtggtgtggatgtaat-atttctctgtttgcactgagttgagatgttgtctt-gcagGCATATTTGTCCGTAGCGTTGATCGTTTCAACGAACAGAGTGAGCATGATGTCCCTGCCGTCGAGAGATCAAACCTCAGGCCATTGCTCGATGAAAACGA
















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|5325067|gb|AI783258.1|AI783258
EST:     TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG                         GCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATG
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATG
EST: gi|71429290|gb|DR810340.1|DR810340
EST:     TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG                         GCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC
EST: gi|6056590|gb|AW090995.1|AW090995
EST:     TCTTATATTGACATNCATCCTTTTCGCTGCAGNTGNGTTCTGGTTCATTG                         GCATATTTGTCCCCAGCGTCGACCGTTT-AACGA
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGA
EST: gi|32907645|gb|CF012458.1|CF012458
EST:     TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG                         GCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAGTATGGCC
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC
EST: gi|78110258|gb|DV528673.1|DV528673
EST:     TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG                         GCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC
EST: gi|5846879|gb|AI999962.1|AI999962
EST:     TCTTATATTGACATCCATCCTTTTCG-TGCAGTTGTGTTCTGGTTCATTG                         GCATATTTG-CCCCAG
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAG
EST: gi|211532277|gb|FL465631.1|FL465631
EST:     TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTMTGGTTCATTG                         GCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC
genomic: TCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCC

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), 48 (downstream exon)
Score: 168

GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 190

GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 155

GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttgtattttgtgataattcagctgaagctgagatgatcttgtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA
                                         tcttgtcttt  CT-rich tract
        tattttgtgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccagtgttcagtagtgagtactagtatatatctgtactatatatatatttgtattttgtgataattcagctgaagctgagatgatcttgtctttgcagGCATATTTGTCCCCAGCGTCGACCGTTTCAACGAAGAGAGCGAATATGGCCTTACTGCCGCTGAGAGATCAAGTATCAGGCCACTGCTTGGTGAAAACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaag