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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgacttttactcctctctaattgaaataatcatgtagttctccaatgaattatcttaatatcatctcttttgctactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT

Basic information

species Zea mays
transcript GRMZM2G120175_T04
intron # 8
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|101381796|gb|EB812955.1|EB812955
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|60354097|gb|DN221070.1|DN221070
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|78120401|gb|DV538785.1|DV538785
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|148934735|gb|EC878784.2|EC878784
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|74234882|gb|DT642796.1|DT642796
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|148943740|gb|EC888810.2|EC888810
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|149085220|gb|EE174728.2|EE174728
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|76287457|gb|DV027025.1|DV027025
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
EST: gi|211152612|gb|FL453073.1|FL453073
EST:     CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAA                         GTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT
genomic: CATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAAT

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: 62

GGAAGCGTCATTTCTGAAATTTGTGGCTTGGTTGTGGTGTTGTCTGGTACCATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 137

GGAAGCGTCATTTCTGAAATTTGTGGCTTGGTTGTGGTGTTGTCTGGTACCATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GGAAGCGTCATTTCTGAAATTTGTGGCTTGGTTGTGGTGTTGTCTGGTACCATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GGAAGCGTCATTTCTGAAATTTGTGGCTTGGTTGTGGTGTTGTCTGGTACCATTTTGTTGCATGTGACGAAGGATTATGAAAGGATCCCACAATCAAGAAgtgtgtgact ... tactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgtagttctccaatgaattatcttaatatcatctcttttgctactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT
                        tcttaat  putative branch site (score: 71)
                                tcatctcttttgct  CT-rich tract
               aatgaattatcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgacttttactcctctctaattgaaataatcatgtagttctccaatgaattatcttaatatcatctcttttgctactatgtagGTGTTTATGCACCATTATCTCCCTCTTTGACAACTAGATTAAATGGAGAATTGTTGAAGCATGTCGTGGATGAGAGGACTTCGGACGAAGAAAAGGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA