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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaacctccttgttaattgaaaatggatggttagtattaggatcatctttttttaatgtcctgaagtatgtctgaactaaagctgggaatgctttcaaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT

Basic information

species Zea mays
transcript GRMZM2G071441_T01
intron # 28
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|211172394|gb|FL129173.1|FL129173
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATG-A--                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|32865867|gb|CF005549.1|CF005549
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|32834007|gb|CD973685.1|CD973685
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|67023760|gb|CO452509.1|CO452509
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|37382211|gb|CF628041.1|CF628041
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|32911283|gb|CF016095.1|CF016095
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|32940265|gb|CF045084.1|CF045084
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|211172392|gb|FL129171.1|FL129171
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATG-A--                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|211172393|gb|FL129172.1|FL129172
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTG
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTG
EST: gi|211172395|gb|FL129174.1|FL129174
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATG-A--                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|91050276|gb|EB160694.1|EB160694
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|37382947|gb|CF628445.1|CF628445
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
EST: gi|88750432|gb|DY534573.1|DY534573
EST:     TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATG                         ATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT
genomic: TGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGT

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: 101

AACCGCCATTCTTTTGAGAAGCCTGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 51

AACCGCCATTCTTTTGAGAAGCCTGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

AACCGCCATTCTTTTGAGAAGCCTGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 66

AACCGCCATTCTTTTGAGAAGCCTGTGAGGATTTACAACTAAAGCTAGGAATACTTTTTACATGCGATGAATGgtgagtaacc ... caaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatgtcctgaagtatgtctgaactaaagctgggaatgctttcaaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT
                        aactaaa  putative branch site (score: 66)
                                       tgctttc  putative PPT
                        aactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaacctccttgttaattgaaaatggatggttagtattaggatcatctttttttaatgtcctgaagtatgtctgaactaaagctgggaatgctttcaaactgcagATGAACAGGATATGAAGCAGTCTTGTTCCAAAAGCAGTCTTTTGGTGATGTACATGGAGCTTTTGCATAGAGTAGTTTATGTGGCAATTATCTCAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT