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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggacttccaagtttggagtttgatttcttgttcgcgaaggatcggattcgaatttgtgtaggttgtaacattgctctatggcttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 19
gtactggacttc-caagtttggagtt--tgatttcttgttcgcgaaggatcggattcgaatttgtgtaggttgtaacattgctctatggcttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG
||||     |   | | ||| ||| |  || ||||||   |  | | ||| | |||  ||         ||   ||  |||    |||| |||||| ||||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||| |||| |||| ||||| |||
gtacaatgttcaactactttagagctcttgctttcttacacttggatgattgaattgaaac-------agtaacaa--ttggctcatggtttcaaatagGCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG
















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|21389890|gb|BQ527939.1|BQ527939
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|33101487|gb|CF061447.1|CF061447
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|5739589|gb|AI947384.1|AI947384
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|60347665|gb|DN214638.1|DN214638
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|21331635|gb|BQ487016.1|BQ487016
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|32909378|gb|CF014190.1|CF014190
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|22715088|gb|BU197571.1|BU197571
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTCCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|60397236|gb|DN230052.1|DN230052
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|6095640|gb|AW120307.1|AW120307
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|9794851|gb|BE553159.1|BE553159
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|5804468|gb|AI979438.1|AI979438
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGCCTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
EST: gi|74237144|gb|DT645058.1|DT645058
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 311

GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 300

GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 308

GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtactggact ... cttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggatcggattcgaatttgtgtaggttgtaacattgctctatggcttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG
                          ttgtaac  putative branch site (score: 308)
              aatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggacttccaagtttggagtttgatttcttgttcgcgaaggatcggattcgaatttgtgtaggttgtaacattgctctatggcttcaaacagGCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG