Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgcttttacctaaacccctttacactagctgacttgtggtcttgttaattattactagcgattgtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG

Basic information

species Zea mays
transcript GRMZM2G112782_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112782_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g14640.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gcatgc-ttttacctaaaccccttt---acactagctgacttgtggtcttgttaattattactagcgattgtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG
                                        ||| | || ||  |  |  | | |   | ||||| | |    | |||||| ||||  ||  ||| |   | || |||||||||||||||||||||| ||| ||||    ||||| ||||||||||| |||||||| |||||| | ||  ||||||||||||| |||||||| || ||||
gtgtgttttgtcctaacatttagttgttgacttactcctacattcattctatattcattcatgtggtagactagtttatccattgtcttgctaatggttggtagtgtccgcct-tgcagTTGGAGCAGTTTGAGAGAGCTATAAGCATGAGCAATGATAAGTATTCTTTGGAAGAGGGTACATTGGCCAGGCGTCGGCAGTTCGTTGTAGCAATGGAGG
















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|148970852|gb|EE021628.2|EE021628
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
EST: gi|76287560|gb|DV027128.1|DV027128
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
EST: gi|149070489|gb|EE158892.2|EE158892
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
EST: gi|211046462|gb|FL097856.1|FL097856
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATNAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
EST: gi|148931764|gb|EC875027.2|EC875027
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
EST: gi|148932521|gb|EC876312.2|EC876312
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
EST: gi|93016784|gb|EB642304.1|EB642304
EST:     ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAG                         TTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG
genomic: ACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTG

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: 47 (upstream exon), 48 (downstream exon)
Score: 55

TAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

TAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

TAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 110

TAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGAACTGCAAAATGGCAGgcatgctttt ... gtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacactagctgacttgtggtcttgttaattattactagcgattgtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG
                        tgttaat  putative branch site (score: 110)
                       ttgttaattattacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgcttttacctaaacccctttacactagctgacttgtggtcttgttaattattactagcgattgtctgtgcagTTGGAGCAGTTTGAGAGGGCTGTAAGTTCAAGCAACGATAAGTATTCATTGGAAGAAGGTACAGTAGCACGGCGTCGGCAGTTTGTTGTAGCCATTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG