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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaaaataaactaatttcccttggaaaaatgaaaaccccttagaaaaatgaggttcccagattagcccttagtgtttacattatgctgttgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG

Basic information

species Zea mays
transcript GRMZM2G053047_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053047_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g43380.1 (Oryza sativa), 3'ss of exon 7
aggaaaataaactaatttcccttg-gaaaaatgaaaaccccttagaaaaatgaggttcccagattagcccttagtgtttacattatgctgttgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG
|  |    |||||  | ||      || |||| |||    |       | |   |||   || |      ||     |     |||||||    ||| |||||||||||| ||||| ||||||||||||||||| ||||| || ||| |||| ||||||||||| |||||||| |||| |
ataagccaaaacttttgtctgaaacgacaaataaaagtgaccggaggtagtacagtttt-agctacttggttgccactactgatatgctgcaattttccagAATGTTTGTAGATGCTCTGGATGCACAAATGTACGACAAACATCATGAAACAGGGCATTGCATATTGAGTCTTCACAGG

upper sequence: GRMZM2G053047_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G06780.2 (Glycine max), 3'ss of exon 11
aggaaaataaactaatttcccttggaaaaatgaaaaccccttagaaaaatgaggttcccagattagcccttagtgtttacattatgctgttgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG
 | ||| |||  | ||||     |  || |  |     |  | | ||  ||   ||   || | |     |  ||    |    | |  ||  | | |||||||||||| |||||| ||||||| |||||||||||  | ||||||  ||| || || ||    |||||  |    || 
-gtaaactaagttcattttgtcagctaagaaaattgttctcttgtaacttg---ttgagagttaaataactgatgcaagc----taccatt--tgtgcagAATGTTTGTGGATGCATTGGATGCGCAAATGTATGATGAACACCATTTAACAGGACACTGTTCTTTGAGCTTGTCAAAA

upper sequence: GRMZM2G053047_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA16G03340.1 (Glycine max), 3'ss of exon 12
aggaaaataaactaatttcccttggaaaaatgaaaa---ccccttagaaaaatgaggttcccagattagcccttagtgtttacattatgctgttgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG
       |||||| | |||  || | ||||| | ||     |  |     ||   | ||   || | ||    |  |||  ||    | |  ||  | | |||||||||||| |||||| ||||||| |||||||||||  | ||||||  ||| || |  ||    |||||| |    || 
------gtaaacttagttcattttgtaaaataagaaaattgctctcttgtaacttgtttgagagttaagtaactgatgtaaac----taccatt--tgtgcagAATGTTTGTGGATGCATTGGATGCGCAAATGTATGATGAACACCATTCAACAGGACGCTGTTCTTTGAGTTTGTCAAAA

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|60342418|gb|DN209391.1|DN209391
EST:     AGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAG                         AATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAAC
genomic: AGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAGgtatgggttt ... tgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAAC
EST: gi|60352494|gb|DN219467.1|DN219467
EST:     AGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAG                         AATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAAC
genomic: AGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAGgtatgggttt ... tgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAAC

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: 50

ATACTCTGTTACATATGCCTAATGATGGAGACACGTGGTCTGTGATGCAAAGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAGgtatgggttt ... tgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG


Block sizes: 34 (upstream exon), 46 (downstream exon)
Score: 18

ATACTCTGTTACATATGCCTAATGATGGAGACACGTGGTCTGTGATGCAAAGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAGgtatgggttt ... tgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

ATACTCTGTTACATATGCCTAATGATGGAGACACGTGGTCTGTGATGCAAAGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAGgtatgggttt ... tgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 14

ATACTCTGTTACATATGCCTAATGATGGAGACACGTGGTCTGTGATGCAAAGTTGGGTTTTGCCTACACGGTCATTCCTAGAATTTGTTATGTTCTCAAGgtatgggttt ... tgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgaggttcccagattagcccttagtgtttacattatgctgttgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG
                                          tgttgat  putative branch site (score: 14)
                                                ttttc  CT-rich tract
                              tttacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaaaataaactaatttcccttggaaaaatgaaaaccccttagaaaaatgaggttcccagattagcccttagtgtttacattatgctgttgattttcagAATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG

- - aaataaa
- - - - - - - - - - - - gaaaaatg
- - - - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctg