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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttagacacatgctgtgcaattatagtaggtattatttagttgaccatgtggtcatgttagaacactagaacgatattaatacctccgttttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG

Basic information

species Zea mays
transcript GRMZM5G824600_T02
intron # 2
splice site 3'
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|148969452|gb|EE020260.2|EE020260
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|149055770|gb|EE156478.2|EE156478
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|148972824|gb|EE023810.2|EE023810
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|32944033|gb|CF048852.1|CF048852
EST:     TCCTCTTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|149107259|gb|EE189142.2|EE189142
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|149001497|gb|EE038802.2|EE038802
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTC-TTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|148930859|gb|EC873272.2|EC873272
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|211403715|gb|FL311339.1|FL311339
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|84980410|gb|DW530759.1|DW530759
EST:     TCCTCTTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|148971977|gb|EE022778.2|EE022778
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|31355494|gb|CD439851.1|CD439851
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|31355047|gb|CD439404.1|CD439404
EST:     TCCTATTCACTGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|31355865|gb|CD440222.1|CD440222
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|211233989|gb|FL398757.1|FL398757
EST:     TCCTCTTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCTGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|149103654|gb|EE289058.2|EE289058
EST:     TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
EST: gi|20811111|gb|BQ295589.1|BQ295589
EST:     TCCTCTTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAG                         GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCTGG
genomic: TCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG

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), 48 (downstream exon)
Score: 522

CGAGGACGTGCAGGTGGCGCCGCCGCAGGCCGGCGAGGTCCGCGTCAAGATCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 605

CGAGGACGTGCAGGTGGCGCCGCCGCAGGCCGGCGAGGTCCGCGTCAAGATCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 325

CGAGGACGTGCAGGTGGCGCCGCCGCAGGCCGGCGAGGTCCGCGTCAAGATCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 335

CGAGGACGTGCAGGTGGCGCCGCCGCAGGCCGGCGAGGTCCGCGTCAAGATCCTATTCACCGCGCTCTGCCACACCGACCACTACACCTGGAGCGGCAAGgtgttgtctt ... ttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtggtcatgttagaacactagaacgatattaatacctccgttttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG
                             tattaat  putative branch site (score: 335)
                                   tacctccgttttct  CT-rich tract
                            atattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagacacatgctgtgcaattatagtaggtattatttagttgaccatgtggtcatgttagaacactagaacgatattaatacctccgttttctatgcagGATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - catgctg
- - - - - - - - - - - - - - - - - - - - - - -catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -catgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacta