Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgcgcgcttcaatttttccggctggcttgcgagaggagcgagcgttacgttgctgttttttttccctttctaacttttgctgtctgctgtgtgcgcgctcgcgtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT

Basic information

species Zea mays
transcript GRMZM2G025231_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 1
gtacgcgcgcgcttcaatttttccggctggcttgcgagaggagcgagcgttacgttgctgttttttttccctttctaacttttgctgtctgctgtgtgcgcgctcgcgtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT
      |  ||  | |    | ||| |||  ||              | ||   ||  |  |||||||    |   |  ||| | | | |  | ||| || |  |||   || ||||||||||||||  ||| |||||||||||||||||||||||||||||||||||||||| || ||   ||||| ||| || || |||||||||||||||||||
------gtacgtgtgagcggtgccg-ctgattttt--------tcttctttttttttttaattttttttgggtctga--tttcgtttttttttttgttcgtggccgc---cgcgcagCCGAAGCCGCTCCGGCAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTGGGGCTCAACCCCGACGGCGAGCCGTTCGTGGCGTGCAACGAGT
















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|149001186|gb|EE038454.2|EE038454
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211344801|gb|FL219951.1|FL219951
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211344804|gb|FL219954.1|FL219954
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|71309263|gb|DR790918.1|DR790918
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211344807|gb|FL219957.1|FL219957
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211342416|gb|FL219947.1|FL219947
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|148963234|gb|EE014221.2|EE014221
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCCGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211344805|gb|FL219955.1|FL219955
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211342409|gb|FL219940.1|FL219940
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211344802|gb|FL219952.1|FL219952
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|211342413|gb|FL219944.1|FL219944
EST:     CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGG                         CCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGAC

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), 47 (downstream exon)
Score: 123

AAGTGGAGGGGAGGAAGCGATGGAGGCGAGCGCCGGGCTGGTGGCCGGCTCCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 264

AAGTGGAGGGGAGGAAGCGATGGAGGCGAGCGCCGGGCTGGTGGCCGGCTCCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 241

AAGTGGAGGGGAGGAAGCGATGGAGGCGAGCGCCGGGCTGGTGGCCGGCTCCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 1417

AAGTGGAGGGGAGGAAGCGATGGAGGCGAGCGCCGGGCTGGTGGCCGGCTCCCACAACCGCAACGAGCTCGTCGTCATCCGCCGCGACGGCGATCCCGGGgtacgcgcgc ... gtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttccctttctaacttttgctgtctgctgtgtgcgcgctcgcgtgcgtgcagCCGAAGCCGCCGCGGGAGCAGAACGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTTGCCCCCGGCGGGGACCCCTTCGTGGCGTGCAACGAGT
          ttctaac  putative branch site (score: 1417)
             taactttt  TA-rich tract