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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgatgcaattttatatattccactttagtatcttgttcactatttctttctttcttggaaatcagtactaatgactagcaaatggacatcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCA

Basic information

species Glycine max
transcript GLYMA09G01820.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------tttgatg--caattttatatattccactttagtatcttgttcactatttctttcttt---cttggaa----------atcagtactaatgactagcaa--atggacatcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCA
|| ||| ||| | || ||||| | | || | ||| | | |||| | || || |||| || ||| || ||| | ||| | || | || |||||||||||||| || || |||||||||||||||||
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagacattatcatgcgtttagcacctcaaatttgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT
















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|192297466|gb|FG992694.1|FG992694
EST:     ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACT                         GCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTAC-TTCC
genomic: ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACTgtgagtactg ... tcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
EST: gi|193566982|gb|FK525083.1|FK525083
EST:     AAAAAGAACCTTTCTAAATACACATTAACACT                         GCATCGACGTATAGTTCAGTACAAGACTGCATATTATTCATTTTACCTTCC
genomic: AAAAAG-ACCTTTCTAAATACACATTAACACTgtgagtactg ... tcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
EST: gi|192325137|gb|FK017523.1|FK017523
EST:     ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACT                         GCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
genomic: ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACTgtgagtactg ... tcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
EST: gi|6567264|gb|AW234875.1|AW234875
EST:     ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACT                         GCATCCACGTATAGTTCAATACAAGACTGC
genomic: ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACTgtgagtactg ... tcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGC
EST: gi|7028813|gb|AW458596.1|AW458596
EST:     ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACT                         GCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
genomic: ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACTgtgagtactg ... tcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
EST: gi|7284732|gb|AW597282.1|AW597282
EST:     ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACT                         GCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC
genomic: ATCACCACATTGGAAGGAGAAAAAGACCTTTCTAAATACACATTAACACTgtgagtactg ... tcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttctttcttggaaatcagtactaatgactagcaaatggacatcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCA
                      tactaat  putative branch site (score: 1)
 tactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgatgcaattttatatattccactttagtatcttgttcactatttctttctttcttggaaatcagtactaatgactagcaaatggacatcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCA

- tgatgca
- - - - - - - - - -ttccact
- - - - - - - - - - - - - - - - -cttgttc