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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtgagttcttcctttacagcgtttgatttcagtattgcatctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA

Basic information

species Zea mays
transcript GRMZM2G180863_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g41360.1 (Oryza sativa), 3'ss of exon 4
--------------gtagtgtgagttcttcct-ttac--agcgtttgatttcagtattgc---atctcgttg--taaattctatctgactacgaattagtgtc---atccttggtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA
                |   |  |||| |  | ||||  |     || |||||||  | |   || |  ||   |  ||   |  || |  | || ||  |     ||| ||| | | ||||||||||||||||||||||||| ||||| ||||| |||||| | ||||||||||| |||||||||||||||||||| ||||| |||||||||||||| ||||
gtactcttaacagaccaagatatgttccttttattacctaaatgctgttttcagttgtacgcaattttcttagctggatctgagttggcagcaaagtaacgattgaatctttgttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTGGTGGTTTCTCCTGATGTGGGTGGTGTTGTCAGAGCACGTGCATTTGCTA
















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|149088668|gb|EE177786.2|EE177786
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
EST: gi|78088529|gb|DV516922.1|DV516922
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCA
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCA
EST: gi|149112871|gb|EE191452.2|EE191452
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACC
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACC
EST: gi|6626351|gb|AW257883.1|AW257883
EST:     CACAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
EST: gi|74240297|gb|DT648211.1|DT648211
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
EST: gi|149006976|gb|EE040195.2|EE040195
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCA
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCA
EST: gi|71770134|gb|DR968071.1|DR968071
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAG
EST: gi|31354391|gb|CD438748.1|CD438748
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
EST: gi|149000114|gb|EE037239.2|EE037239
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGAATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
EST: gi|149079724|gb|EE168725.2|EE168725
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCA
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCA
EST: gi|50322471|gb|CO517597.1|CO517597
EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

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: 140

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 196

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA
                 atctgac  putative branch site (score: 196)
         taaattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgtgagttcttcctttacagcgtttgatttcagtattgcatctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA