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

...aatctgcaatcccatctgaagggcctaggtgcttttggcaatagttaatgcaccgctgacaaaaaagaatggtgttactgaaatgctacttggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTGAACCCTAAAAACAAGCCTGGAAGAATTACAGTCATTGTTAGAATGGGAG

Basic information

species Glycine max
transcript GLYMA15G06020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G33510.2 (Arabidopsis thaliana), 3'ss of exon 3
aatctgcaatcccatctgaagggcctaggtg---cttttggcaatagttaatgcac-cgctgacaaaaaagaatggt-gttactga--aatgctacttggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTGAACCCTAAAAACAAGCCTGGAAGAATTACAGTCATTGTTAGAATGGGAG
          |   | | || |   | ||     | ||    |   | ||   ||     |   |  | | ||||   | |  |||   |||    ||| |   |||||||||||||| ||||| ||   |||||| |||||||||||||| || || |||||| | |||||||||||||| ||||| || || || ||||||||||
-----attgcctggtattaaagatattggaaaaccattacaaagaggctacaacagatttttgtatgagaaaatgacagatgttgattgatgtactttgat--gcagGTGAGTGATAAAATGGTCCCTAGTGAACTGGTTAAGCTGATAGAGATACTAAACCCTCAGAACAAGCCTGGAAGGATTACGGTTATAGTGAGAATGGGAG
















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|6916081|gb|AW397611.1|AW397611
EST:     TTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: TTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|8825878|gb|BE209608.1|BE209608
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|192329375|gb|FK021829.1|FK021829
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|7796655|gb|AW782052.1|AW782052
EST:     TTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: TTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|6915150|gb|AW396611.1|AW396611
EST:     TTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: TTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|22524982|gb|BU083793.1|BU083793
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|9819280|gb|BE554793.1|BE554793
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|207761194|gb|GD733313.1|GD733313
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|298190989|gb|HO038468.1|HO038468
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCACCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|308098317|gb|HO760058.1|HO760058
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|20498272|gb|BQ273202.1|BQ273202
EST:     GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
EST: gi|105633416|gb|DW246779.1|DW246779
EST:     GTGCTCATGTTGAATGCTTGAGAGGAGTTGCTANTCCACTTGGCATCAAG                         GTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG
genomic: GTGCTCATGTTGAATTCTTGAGAGGAGTTGCTAATCCACTTGGCATCAAGgtgcatataa ... tggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgcaccgctgacaaaaaagaatggtgttactgaaatgctacttggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTGAACCCTAAAAACAAGCCTGGAAGAATTACAGTCATTGTTAGAATGGGAG
        cgctgac  putative branch site (score: 3)
                                                ttttc  putative PPT
               aaaaaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgcaatcccatctgaagggcctaggtgcttttggcaatagttaatgcaccgctgacaaaaaagaatggtgttactgaaatgctacttggttttcagGTGAGTGATAAGATGGTTCCCGATGAACTTGTTAAGCTGATAGATATTCTGAACCCTAAAAACAAGCCTGGAAGAATTACAGTCATTGTTAGAATGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - caatccc
- - - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctact