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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccactgacttccttatcctgatgaaactatctatgccatattctttcttatcctgatatggctagtgttatcttggtgtctgattcctggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA

Basic information

species Zea mays
transcript GRMZM2G132712_T03
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os08g40530.2 (Oryza sativa), 3'ss of exon 5
gtccactgacttccttatcctgatgaaactatctatgccatat-tctttcttatcctgatatggctagtgttatcttgg---tgtctgattcctggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA
| ||| |  ||  |||| | || | | |   ||||||   | | | |   || |||     ||  |  ||||||||  |   ||| ||||| ||  ||||  ||| ||||| |||||||||  |||| |||||||||||||||||  | ||||||||||||||||||||||||||| || | ||||| || |||||| | ||||
ggccattt-ctgtcttaacatgctaaga---tctatgatctgtgtatgatttgtccctggttgcttcatgttatctcagtgctgtttgattgctacaattgcagTCAGATGCTGGTGTTCATGTCCATTGGAAAGGTGCAGCTGAGCTTGTGTTATCATCTTGCAAAAGCTGGCTTGCCCTGGATGGTTCAGTTCAGCCCATGA
















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|211422272|gb|FK992813.1|FK992813
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422266|gb|FK992807.1|FK992807
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422265|gb|FK992806.1|FK992806
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422271|gb|FK992812.1|FK992812
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422274|gb|FK992815.1|FK992815
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422270|gb|FK992811.1|FK992811
EST:     ATGTTTTTCCATTTAACTCGGAGAANAAACGTGGCGCTGTTGCAGTACAG                         TTANATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422268|gb|FK992809.1|FK992809
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422273|gb|FK992814.1|FK992814
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|211422275|gb|FK992816.1|FK992816
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|31350151|gb|CD434508.1|CD434508
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
EST: gi|71443249|gb|DR824299.1|DR824299
EST:     ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG                         TTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA
genomic: ATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTA

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: 45 (upstream exon), 49 (downstream exon)
Score: 69

ATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 120

ATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 106

ATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 77

ATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAGgtactacata ... ggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttatcctgatatggctagtgttatcttggtgtctgattcctggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA
                                               aatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccactgacttccttatcctgatgaaactatctatgccatattctttcttatcctgatatggctagtgttatcttggtgtctgattcctggaattttagTTAGATGATGGTGTTCACATCCACTGGAAAGGTGCAGCTGAAATAGTGTTATCATCTTGCAAAAGCTGGCTTTCCGTCGATGGCTCTGTTCAGTCAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- ccactga
- - - - - - - - - cctgatg
- - - - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc