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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagatcacctcagtatcataaactgctcaaactataaaacatacaagtttgtccattgctagttagatgggcataggctaatttcatgatgtgaaattctgcccatcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC

Basic information

species Zea mays
transcript GRMZM2G359018_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G359018_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 3'ss of exon 2
gtaaga---gatcacctcagtatcataaactgctcaaactataa-aacatacaagtttgtccattgctagttagatgggcataggctaatttcatgatgtgaaattctgcccatcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC
||||||     |  | ||  ||||| ||  || ||||  | |   ||   | ||   ||| |      || |||||    | |    |  |   |      ||| | ||||| |   ||||||||||||||   ||||||||||||| | ||||| |||||||| ||||||||||||||  |||| || |||||||||||||||||||||||||| ||||| 
gtaagattgtttttcatctctatcacaacttgttcaagttttggcaaagcataatcatgttccac---aggtagataattacataaaaggtctct------aaactgtgccctttctttcagGTCTCCCCCGCGGATCCCAGAGGTGATTATTCCAGAAGATTTGGTTGTCAACATTGCTCTATCTACACGTTATGAGATCAACAGGGCCTTTGCCAATCTT
















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|88757769|gb|DY541910.1|DY541910
EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
EST: gi|29543942|gb|CB604322.1|CB604322
EST:     TGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
EST: gi|32934217|gb|CF039029.1|CF039029
EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
EST: gi|60395596|gb|DN228466.1|DN228466
EST:     TCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
EST: gi|31355597|gb|CD439954.1|CD439954
EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
EST: gi|22546350|gb|BU098661.1|BU098661
EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
EST: gi|29543376|gb|CB603772.1|CB603772
EST:     TCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

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), 47 (downstream exon)
Score: 239

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 68

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttagatgggcataggctaatttcatgatgtgaaattctgcccatcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC
                ggctaat  putative branch site (score: 68)
                   taatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagatcacctcagtatcataaactgctcaaactataaaacatacaagtttgtccattgctagttagatgggcataggctaatttcatgatgtgaaattctgcccatcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA