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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttttttactatcactgcccatttcctctatttgcagcgttcacctacaagtttcaacagtacatctgcactattggtaaagctactttccaag...

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 12
TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtttttttta--ctatcactgcccatttcctctatt---tgcagcgttcacctacaagtttca-acagtacatctgcactattg-gtaaagctactttccaag
||||||||||||||||||||||||| ||||||||||| || || |||||  | || ||||| || ||||| || |||||||| || |||||||||||||||||||| | || |   || | | |    ||||  |  |       |||     | |     | ||   |  | |||||  |   |||  ||   | |          
TGGCTGCATTCCCTTCAGCTAAGCCCCCACTGGGAGTATTCTTTGCAGCTGTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatattctgacctcttagttattatttatttaaaaggacacagatggtatccttgtgcttggcaaggaacatccacttcattttgtggggttcaa-------
















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|20506752|gb|BQ279326.1|BQ279326
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32928790|gb|CF033602.1|CF033602
EST:     CGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: CGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|194716812|gb|FK933971.1|FK933971
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32921358|gb|CF026170.1|CF026170
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32832538|gb|CD972216.1|CD972216
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32929828|gb|CF034640.1|CF034640
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|67024128|gb|CO452877.1|CO452877
EST:     ATAGCTCCTCGTCTGCAACCCCGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|22819046|gb|BU499136.1|BU499136
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAAATCAT
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCAT
EST: gi|32921381|gb|CF026193.1|CF026193
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|211465905|gb|FL134197.1|FL134197
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32835489|gb|CD975167.1|CD975167
EST:     GATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: GATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32928791|gb|CF033603.1|CF033603
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
EST: gi|32920698|gb|CF025510.1|CF025510
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC

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: 631

TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 776

TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1039

TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1272

TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttt ... gtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagttttttttactatcactgcccatttcctctatttgcagcgttcacctacaagtttcaacagtacatctgcactattggtaaagctactttccaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC