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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaaatctattctattaaaacttaaaacaaagatagttcctagtaaaaggtttttttttctttcgatttttagtcccttacgatttttacaatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAATGGCACTGGATCATTCATTGAAATCATATACGTGTTAATCTTCATCGTA

Basic information

species Glycine max
transcript GLYMA06G12740.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G12740.4 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g15330.t01 (Vitis vinifera), 3'ss of exon 3
---------tcaaaatctattctattaaaacttaaaacaaagatagttcctagtaaaaggtttttttttctttcgatttttagtcccttacgatttttacaatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAATGGCACTGGATCATTCATTGAAATCATATACGTGTTAATCTTCATCGTA
         |   |  ||||||  || ||  |       | |    |   ||   || | |   || | |||||    ||    ||  || || |    |||   ||||||||||  | || ||||| ||     |||||||| | ||||| ||  | |||||||||||| ||  ||||||||||||||| ||| | |||||||||| |
agaacaatatttcatcctattcctttgaatttctctggcacgcccttcagtatggaaggctccattatactttctgagtt--accctctatgaat----caa---acagGTATGGCCTTCCATTTGTATCAAAGAACAACATACTGGTGTCCACCATCAATGGCACTGGAGCAGCCATTGAAATCATATATGTGCTCATCTTCATCGCA
















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|298197426|gb|HO044905.1|HO044905
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|209700762|gb|BW683045.1|BW683045
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|298168790|gb|HO009720.1|HO009720
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|298171821|gb|HO021413.1|HO021413
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|192326194|gb|FK016986.1|FK016986
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|298191089|gb|HO038568.1|HO038568
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|298190375|gb|HO032496.1|HO032496
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAATGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|298175722|gb|HO018319.1|HO018319
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA
EST: gi|151413261|gb|EV283069.1|EV283069
EST:     TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTG                         GTATGGTTTGCCTTTTGTGTCTCCCCACAACATACTAGTGTCAACAGTGAA
genomic: TCGGGCATTCCATATGTCATGACACTGCTCAATTGTCTCCTTTCAGCTTGgtgagcttct ... caatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaggtttttttttctttcgatttttagtcccttacgatttttacaatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAATGGCACTGGATCATTCATTGAAATCATATACGTGTTAATCTTCATCGTA
                              cccttac  putative branch site (score: 3)
                                       tttttac  putative PPT
      tttttttttctttcga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaaatctattctattaaaacttaaaacaaagatagttcctagtaaaaggtttttttttctttcgatttttagtcccttacgatttttacaatccacagGTATGGTTTGCCTTTTGTGTCTCCCCACAACATATTAGTGTCAACAGTGAATGGCACTGGATCATTCATTGAAATCATATACGTGTTAATCTTCATCGTA

-caaaatc
- - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - gttccta