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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA

Basic information

species Glycine max
transcript GLYMA18G01590.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 5
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
                                             || ||    ||||    |||     |   |      |||||| |||||  |  ||| | | ||  |||  | ||    | || |||          ||| || |    ||| | || ||| | |  ||||  |     |  | ||||| |||||||| |||||| ||||||| ||||||||||| ||||| || |||||||||||||  ||||| ||| ||||||| || |||||||| || || |
-------------------------------------------gttgtgtagttatttgagagcatggagaattattccttactaaattatttcctaattc-tgaatgcttttcttagt--gttgtgtaatt---------tttttgagaaacatgtt-cttattgtgtgttaacgtg-----tctttcagGTCAGTCATCACCCAATGGTTGTTGCATGTCACTGTGAAGGAAGAGGTTGGAAGTTTTGGGGGGATTCAAATCTGAAAGGGAAGTTCTGGGGTCGATCAA

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
                   || |   | ||||    | ||   ||||    ||  | ||  |  ||||   |||  |||     ||||  |||    |||||||||  | ||   |   | |  |  | |||    ||  |    |    ||| |  ||| |   |  ||||         |||| || |||| ||||||||||| |||||||||||||| || |||||||||   || ||||| || |||| ||| || ||| | ||||||||||| ||||| || || |
-----------------gcaagtcaaccatcaca--tcattctaatgtag-aagttgtattgaaaaatcatgcatgaat--gtgaaaaactttaacacttcattatctttttaaatctatcagac--atatataatagcaacccct-caccttct-ttgccaccataattct---------cttgttc-agGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgct--ccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
                                                                                              ||        || |   ||||  | |  |  | |   |  ||| |      | |    ||  |  || ||| | ||||||||||  ||||| |    |||| ||||| || ||||||||||||||||| ||||||||||| || || |||||||| |||||||| |||||| | ||||| || |||||||| ||||| |
--------------------------------------------------------------------------------------------cattcaggttccatagaaatttgg-gctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtaactgggtttttccttt-aacttttcaatcaaggttaatgg-----gaatgagtcaaaatttacaggcaaatgcagcaacaataaacta---aaatatttgt---tgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
  || |   |||||||  ||| || | |   ||     ||  ||      | |   |||  |  |   || |   |     ||   | || |    | || || ||   |||| | |   | | | || ||    ||| | |  |  ||| |           ||| | | |  |  ||||  | |  ||       |    ||||| || ||||||||||||||||| || |||||||| ||||| || || ||||| |||||||  ||    || |||||| | || || ||||| |||||||
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattag-aaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttca-------tctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgtttt-gttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
                                                                                   | ||| ||||    |||||  |     | |  | |  | ||| || | |    ||    | |  |||| || |  |  || |||| || | |        ||  | ||||| ||||||||||||||||||||||| || || || ||||| || || ||||  || ||||  ||    || |||||| | || || ||||| |||||||
---------------------------------------------------------------------------------ctttaaacatttcgaacttcagaacataatatgagctaattaatttgca-tcttccatc--tctacgtgtttt-tatttttatttttattttta-------ttttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA

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|193335307|gb|FK301435.1|FK301435
EST:     CCTACGAAGCTGACTATCCAGATAAAGGACTTAAG-TTTTTTCTGAAAAG                         GTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGG
genomic: CCTACGAAGCTGACTATCCAGATAAAGGACTTAAGTTTTTTTCTGAAAAGgtaactgggt ... cttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGG
EST: gi|8282551|gb|BE020112.1|BE020112
EST:     CCTACGAAGCTGACTATCCAGATAAAGGACTTAAGTTNTTNTCTGAAAAG                         GTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGG
genomic: CCTACGAAGCTGACTATCCAGATAAAGGACTTAAGTTTTTTTCTGAAAAGgtaactgggt ... cttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
                                ttctaac  putative branch site (score: 1)
                                             cttgctcc  putative PPT
                        taattttcttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA