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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACAAACCCGCCTTACTTTATCCACCTGTGTTACAAACCCCGCGGTGGTGACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatactttcaacaccgaatacttgatttttggatgctcgattcacctctgtcgtctccag

Basic information

species Zea mays
transcript GRMZM2G043893_T01
intron # 4
splice site 5'
intron type U2

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|89247433|gb|DY619219.1|DY619219
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|101393107|gb|EB818484.1|EB818484
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|148958192|gb|EC904397.2|EC904397
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|148991871|gb|EE033465.2|EE033465
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|149001041|gb|EE038290.2|EE038290
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|71774294|gb|DR972172.1|DR972172
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|149076392|gb|EE165010.2|EE165010
EST:     CGTCAGGAGGAAGCTGGCTCTTGTTGGAAAAGGCATAACATTNGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: CGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|71758309|gb|DR956246.1|DR956246
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|76913694|gb|DV165227.1|DV165227
EST:     CATAACATTTGACAG                         CGGGGGCTACAACATCAAGGGCCGTACCGGTCGCCACCATCGAGCTCATGA
genomic: CATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAA-GGCCGTACCGGTCGCCACCATCGAGCTCATGA
EST: gi|89252259|gb|DY624045.1|DY624045
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTGCCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|71318207|gb|DR795866.1|DR795866
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
EST: gi|74236861|gb|DT644775.1|DT644775
EST:     GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAG                         CGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA
genomic: GACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAA

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: 24 (upstream exon), 26 (downstream exon)
Score: 1

AGACAAACCCGCCTTACTTTATCCACCTGTGTTACAAACCCCGCGGTGGTGACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAAAAAGGACATGGGAGGCGCGGCGGCGGTGTTTGGTGCAGCAGAGGTTTTG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 55

AGACAAACCCGCCTTACTTTATCCACCTGTGTTACAAACCCCGCGGTGGTGACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAAAAAGGACATGGGAGGCGCGGCGGCGGTGTTTGGTGCAGCAGAGGTTTTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 75

AGACAAACCCGCCTTACTTTATCCACCTGTGTTACAAACCCCGCGGTGGTGACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAAAAAGGACATGGGAGGCGCGGCGGCGGTGTTTGGTGCAGCAGAGGTTTTG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 23

AGACAAACCCGCCTTACTTTATCCACCTGTGTTACAAACCCCGCGGTGGTGACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatac ... tcgtctccagCGGCGGCTACAACATCAAGGCCGTACCGGTCGCCACCATCGAGCTCATGAAAAAGGACATGGGAGGCGCGGCGGCGGTGTTTGGTGCAGCAGAGGTTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACAAACCCGCCTTACTTTATCCACCTGTGTTACAAACCCCGCGGTGGTGACGTCAGGAGGAAGCTGGCTCTTGTTGGGAAAGGCATAACATTTGACAGgttcgtatactttcaacaccgaatacttgatttttggatgctcgattcacctctgtcgtctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG