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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccactattggcagaatagggctttaattcagctgctaattttccttggaattagtcccttttagtgtttcctgtttgatgatccattgtatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA

Basic information

species Zea mays
transcript GRMZM2G415846_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G415846_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g47350.2 (Oryza sativa), 3'ss of exon 15
------aaccactattggcagaatagggctttaattcagctgctaattttccttggaattagtcccttttagtgtttc-ctgtttgatgatccattgtatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA---
      ||  | | |||   |||||     ||   | |||||   |  ||  |    ||||  |  || || |  | | |||||   ||    ||||   ||||||||||||| || ||||||||||||| ||||||| ||||||||||||||||||  ||  | ||||| ||||  || || ||   ||| |  ||| | || |||   
tttaaaaaagagtcttgtt-gaatatataattg--tgagctgtccacattattacatattatacatttatactaatgctctgttc--tgtctgattgc--cctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAACAATTATAACAGTGATGTTGATGATGA---GCTAGTGGACCTCGATGCACCT
















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|211144259|gb|FL374578.1|FL374578
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|94472530|gb|EB701488.1|EB701488
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|78545057|gb|DV622555.1|DV622555
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|93283859|gb|EB676123.1|EB676123
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCT
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCT
EST: gi|6827508|gb|AW331151.1|AW331151
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|211461035|gb|FL374793.1|FL374793
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|211216852|gb|FL374182.1|FL374182
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|6918320|gb|AW399850.1|AW399850
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|211336627|gb|FL399697.1|FL399697
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|211405623|gb|FL391563.1|FL391563
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
EST: gi|14245072|gb|BG873654.1|BG873654
EST:     CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAG                         ATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG
genomic: CTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAG

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: 305

AAGATGCAGTTGAATCCGATCTATCGAAGGCATTTGGAGGACTTAATAGGCTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 204

AAGATGCAGTTGAATCCGATCTATCGAAGGCATTTGGAGGACTTAATAGGCTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

AAGATGCAGTTGAATCCGATCTATCGAAGGCATTTGGAGGACTTAATAGGCTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 305

AAGATGCAGTTGAATCCGATCTATCGAAGGCATTTGGAGGACTTAATAGGCTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttgactat ... tatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggaattagtcccttttagtgtttcctgtttgatgatccattgtatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA
                             gtttgat  putative branch site (score: 305)
     aattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccactattggcagaatagggctttaattcagctgctaattttccttggaattagtcccttttagtgtttcctgtttgatgatccattgtatcctgcagATATATACGGCCAAATTTTGAGTTCTGGTCCTTGGTCAAGACGACATACAGTAACGACAACAGCGATGAGGACGACGAAGAGCTTGGCGACATTGACGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - gctgcta