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

...gcaaaggggagtgattccttgatcgttgattagtttgtttttataattcaggtgtgttgtttgcattagggtgttatgactaatgtattctatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTTGTTGACAAAGGTGGGAATCACATTGAAATGGGATTGCATGTTTTCTTTG

Basic information

species Glycine max
transcript GLYMA10G30220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 3
gcaaaggggagtgattccttgatcgttgattagtttgtttttataattcaggtgtgttgtttgcattagggtgttatgactaatgtattctatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTTGTTGACAAAGGTGGGAATCACATTGAAATGGGATTGCATGTTTTCTTTG
          ||| || ||   || |   |||||| |||| |||| || |      ||| || |||    |||| || |    || ||| |    ||||||||||||| ||||| || ||  | || |||||||||||||| || |||||||| || | | ||||||| || |||||||||||||| ||||||||||| |
----------gtgtttactcc-tcttctgttagtt-gtttatatatttgat-----ttggttacatacatgtgtaatcatcg-tg-attgt----ttcagGTGGATATATATGATTCGAGGACATTCATTGGTGGCAAAGTGGGTTCTTTTGTAGATAGACGTGGGAACCATATTGAAATGGGATTACATGTTTTCTTCG

upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------------------gcaaaggggagtgattccttgatcg--ttgattagtttgtttttataattcaggtgtgttg--tttgcattagggtgttatgact-----aatgtattctatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTTGTTGACAAAGGTGGGAATCACATTGAAATGGGATTGCATGTTTTCTTTG
                                                                                  |       |  || |   || |  ||   | |  || ||||| | ||  | | || ||  ||| ||| |||     ||   |     ||||  ||   |  ||||||| ||||| |||||||||||  |||| |||||||| ||||| |||||||||||||| | | |||| |||||||||||||||||| |||| || |||||||
gtttggattatatatgtaaagatatgttggatgtatctttggcatttatcatactttcaaacaaaacatgaattagtttttcagctaagtttgtttcaaaatggaattcccttggatgatttta-attttggctttgctgattttccatcaggagaaaattggtttataaatggtttggtttgttcagGTAGATATATATGAGTCAAGGTCTTTCATTGGTGGAAAAGTGGGCTCTTTTGTTGATAGACGTGGAAATCACATTGAAATGGGACTGCACGTGTTCTTTG
















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|192300731|gb|FG991113.1|FG991113
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
EST: gi|193532831|gb|FK492833.1|FK492833
EST:     CAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
genomic: CAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
EST: gi|213589825|gb|DB969618.1|DB969618
EST:     GACTTGCAGGTATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
EST: gi|151401347|gb|EV271161.1|EV271161
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGAGGCAAAGTTGGCTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
EST: gi|209717713|gb|BW671531.1|BW671531
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
EST: gi|209702720|gb|BW652763.1|BW652763
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
EST: gi|192300798|gb|FG989710.1|FG989710
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAG                         GTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGCCATGAGgtttggctcc ... tatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaggtgtgttgtttgcattagggtgttatgactaatgtattctatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTTGTTGACAAAGGTGGGAATCACATTGAAATGGGATTGCATGTTTTCTTTG
                                gactaat  putative branch site (score: 2)
                                          ttctatc  putative PPT
                                   taatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaggggagtgattccttgatcgttgattagtttgtttttataattcaggtgtgttgtttgcattagggtgttatgactaatgtattctatcattcagGTGGATATCTATGAGTCAAGACCTTTTATTGGTGGCAAAGTTGGCTCTTTTGTTGACAAAGGTGGGAATCACATTGAAATGGGATTGCATGTTTTCTTTG

- - - gggagtg
- - - - - - - ttccttg
- - - - - - - - - - - - - - - - - - - - - - - - - ggtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattc