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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactgttagcatcaatgcatttcaaaatcatttgtgtgttagttccttcagtttcttttctgttctctttttctgttgagaaaagctatatgttttctttcttcatcattgttttgtgtcttttaatcatgtttcaacgggtcatatatctaaattatatcgtcccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA

Basic information

species Zea mays
transcript GRMZM2G167932_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167932_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g03890.2 (Oryza sativa), 3'ss of exon 7
gtgactgttagcatcaatgcatttcaaaatcatttgtgtgttagttccttcagtttcttttctgttctctttttctgttgagaaaagctatatgttttctttcttcatcattgttttgtgtcttttaatcatgtttcaacgggtcatatatctaaattatatcgtcccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA
                                                            |||| | ||   || | |     || ||  ||| |  || | ||||    |||  ||        |||||||| ||  || ||||||||  ||||||  | | | |   ||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||| || ||||| |||||||||||||
------------------------------------------------------------tctgctttcccctttttt-----aatgcactatatggtcatccttcgc--ttgaattag------taatcatggtttgacaggtcatatg-ctaaatctt-ttgccaattttcagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGCGGAAGCCTAACAGCGGCATAAGAGGTGGAA
















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|31351085|gb|CD435442.1|CD435442
EST:     ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
genomic: ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
EST: gi|31354051|gb|CD438408.1|CD438408
EST:     ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
genomic: ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
EST: gi|22542391|gb|BU092829.1|BU092829
EST:     ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACCCAATGCGTTAAAG                         GCTTCACCCATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
genomic: ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
EST: gi|8367891|gb|BE050836.1|BE050836
EST:     ATGCTTTCG-GGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
genomic: ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
EST: gi|32847652|gb|CD987333.1|CD987333
EST:     ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG                         GCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG
genomic: ATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAG

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: 340

GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 246

GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 292

GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAGgtgactgtta ... cccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttaatcatgtttcaacgggtcatatatctaaattatatcgtcccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA
                             atctaaa  putative branch site (score: 222)
                                            tcccatttt  putative PPT
                       tcatatatctaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactgttagcatcaatgcatttcaaaatcatttgtgtgttagttccttcagtttcttttctgttctctttttctgttgagaaaagctatatgttttctttcttcatcattgttttgtgtcttttaatcatgtttcaacgggtcatatatctaaattatatcgtcccattttagGCTTCACCAATTGAAATAAATGGGCGGCAGATATATGTTGAGGAGAGGAAGCCAAATAGCGGAATAAGAGGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA