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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaatttataatctctctttattgtgagtttattatgttgcttttcaacttctatataatatattacttgtcattctacgtttctgaagcacgaagt...

Basic information

species Zea mays
transcript GRMZM2G108919_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108919_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 3
GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaatttataatctctctttattgtgagtttat-tatgttgcttttcaacttctatataatatattacttgtcattctacgtttctgaagcacgaagt
|||| || |||||    |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||||||||||||   | | |  |         |   | ||| | | | |       | |||  || | | |      | |      |    | | | | 
GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAATgtaagaatttataaagacccatactctctctcacacacacgtttcatatgatggaaactgtaagctactccctcggtcccaaaaggaatttcactctagg-
















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|211527900|gb|FL308285.1|FL308285
EST:     CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|9731847|gb|BE510599.1|BE510599
EST:     CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCCTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|211180712|gb|FL314038.1|FL314038
EST:     CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|7135303|gb|AW498018.1|AW498018
EST:     CAGNTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|211270122|gb|FL340668.1|FL340668
EST:     CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|211177618|gb|FL479926.1|FL479926
EST:     CTGAGGCGAAGGAGCCAGGTGGATGCCCGGTCCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CTGAGGCGAAGGAG-CAGGTGGATGCCCGGT-CTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|60399607|gb|DN232418.1|DN232418
EST:     CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
EST: gi|60351908|gb|DN218881.1|DN218881
EST:     CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: CAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT

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: 197

GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 188

GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaattt ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATgtaagaatttataatctctctttattgtgagtttattatgttgcttttcaacttctatataatatattacttgtcattctacgtttctgaagcacgaagt

- - - - - - - - - -  CAGCTG
- - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - GGTGGA