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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA

Basic information

species Glycine max
transcript GLYMA15G13910.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 8
tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcattt---ttaatttaaattgtgaatttgtg-gtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
     ||  | | | | ||| |  || |  ||  |   |    ||||||   | |   ||||||   ||| ||    |  | || || |         |||||||||||||| || ||||| |||||||| || |||||||| |||||||||||||| ||||| 
---aatgctttagttgcact-agtatttttctgtactcatttattcataacaattgtgtcatttccattatttgtggtgatcaacttatatactgtctttgtagGTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
--tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
   |       |  | | |  ||      |  | |  |       | ||  || | |  | ||  |  | |||   |       ||    ||   | |  ||| ||| ||||||||||| ||||| ||||| ||||| || ||||| |||||||| ||||| 
tcaccaagttctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacata-acttttgctaacttcattacaatgtc-catacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------------tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
                                       || |||| || ||  |   |       |   |  |||   |  |  |  || |  |   ||   |    |    || |     |   |         ||||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||||| ||||  
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAG-ATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
tcttgtgaatgaatcgtacttaagatgta--acttcaacaaaaccttcatacttagtt----gatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
   | ||| | | |   |   ||||||||  | || ||  |    | | |   |   |     || |  |  | ||  || |||  ||||  |    || ||| |||| ||||||||||||||||||||||| || |||||||| |||||||||||||| || |||
--ctttgagttactt-catcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgt--attta-gtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA

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|12772188|gb|BG237115.1|BG237115
EST:     GCCATATCTGCTAT-GCTTGGGGAACAGAAACTTGTCCAAAG                         GTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATG
genomic: GCCATATCTGCTATGGCTTGGGGAACAGAAACTTGTCCAAAGgtggctagct ... aaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATG
EST: gi|254340468|gb|GR850770.1|GR850770
EST:     GCCATATCTGCTATGGCTTGGGGAACAGAAACTTGTCCAAAG                         GTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATG
genomic: GCCATATCTGCTATGGCTTGGGGAACAGAAACTTGTCCAAAGgtggctagct ... aaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
                 ttttaat  putative branch site (score: 3)
     ttagttgatcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
tcttgtg
- - - - - - - - - - - - - - - - - - caaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg