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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcggttttctgtccagaatttactttgcttatagtttagatgcccatccctgttaatgatcatttgttccaattgaaactcttattttatggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA

Basic information

species Zea mays
transcript GRMZM2G112793_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------------------tatcggttttctgtccag---aatttactttgcttatagtttagatgcc-catccctg--ttaatgatcatttgttccaattgaaactcttattttatggt---tgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
                                                                                         || | |||||||  ||   | |||  |||  |||| || |   || |  |    ||  ||| | ||   |   |  || ||||| | |||||||||| |   |||||||||||||||| ||||||||||| ||||||||| |||| ||
gtgctgttcaacttttctcaatgactatgtgcagacttggccgcaattttctcagttgattagaaatttgagcaaatttgttgaattcttctggtttctgtttagcacagtttgtttta-ttatcgtctgtctgtcataatggtgaattagttatgtctatgttaaactgaaaatattattttatgatgattgcagATCACACAGGTTTATGGATTCTACGACGAATGTTTACGAAA

upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------tatcggttttctgtccagaatttactttgcttatagtttagatgcccatccctgttaatgatcatttgttccaattgaaactct-------tattttatggttg------cagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
                                                                |||   | | |          |  | || |   | | | | || |  |  |  | || ||    |  | |  |||||    ||        ||||||||||        |||||||| ||||| ||||| ||||||||||||||||| || ||
gtaattttttggattcatgacactggcggaactctcatcctttttgagttacacctttcgtagcatcttatctgtagtggtgggattttctgttgccattctggttggctttggccatcaaagaatgctcttccttattgaggtcctgatgtgtcattttatggtgtttatatcagATCACCCAGGTATATGGTTTCTATGACGAATGTCTTCGGAA
















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|22818811|gb|BU498901.1|BU498901
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
EST: gi|22490124|gb|BU050047.1|BU050047
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
EST: gi|211043271|gb|FL204511.1|FL204511
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAAC-ATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTC
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTC
EST: gi|211046223|gb|FL204516.1|FL204516
EST:     GGTACCCACATCGAATTACGATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATGCTATGACGAATGTCTACGCAA
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
EST: gi|211046224|gb|FL204517.1|FL204517
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAAGTATGGC
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAAGTATGGC
EST: gi|78118757|gb|DV537141.1|DV537141
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
EST: gi|26559743|gb|CA831978.1|CA831978
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGGGTATGGATTCTATGACGAATGTCTACGCAAGTATG
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAAGTATG
EST: gi|211043270|gb|FL204510.1|FL204510
EST:     GTACCCACATCGAATTACAATCCTTCGTGGAAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTTATGG
genomic: GTACCCACATCGAATTACAATCCTTCGTGGAAA-CCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGT-ATGG
EST: gi|211046225|gb|FL204518.1|FL204518
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAMACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTAT
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTAT
EST: gi|31360213|gb|CD444570.1|CD444570
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
EST: gi|87153205|gb|DY397994.1|DY397994
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
EST: gi|22541924|gb|BU092362.1|BU092362
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGT
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGT
EST: gi|211046226|gb|FL204519.1|FL204519
EST:     GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG                         ATCACACAGGTGTATGGATTCTATGACG
genomic: GGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACG

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: 309

CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 188

CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAGgtacaatcaa ... atggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatccctgttaatgatcatttgttccaattgaaactcttattttatggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA
       tgttaat  putative branch site (score: 188)
                                aaactcttattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcggttttctgtccagaatttactttgcttatagtttagatgcccatccctgttaatgatcatttgttccaattgaaactcttattttatggttgcagATCACACAGGTGTATGGATTCTATGACGAATGTCTACGCAA

- - - ttttctg
- - - - - - - - - - - - -tttgctt
- - - - - - - - - - - - - - - - - - - - - - -ccatccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatttg