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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaattgtttgtttcatttcaatggccattgaagtgaaatcaaatcatatgcttaatatatcattgcccttatgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC

Basic information

species Glycine max
transcript GLYMA16G04560.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtaattgtttgtttca---tttcaa--tggcc--attgaagtgaa-atcaaatcatatgcttaatatatcattgccctt----atgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC
|||||| |  |||    ||    ||| |   |||     || | |||   | | ||||  |  || |||      |     ||    ||| | |||  | | ||||||||||||||||||| || ||||| || ||||||||| |||||||  | ||||||||||| ||||| || || ||  |||| ||||   |||||||||
gtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagc-agGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC

upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtaattgtttgtttcatttcaatggccattgaagtgaaatcaaatcatatgcttaatatatcattgcccttatgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC
||||||||    |  |  || |    |      | | |     |  || ||  ||   ||| | | ||     |||||        ||| |||||||||||||||| || || |||||||||||||| ||| |||||||  | ||||  || || ||||||||||| ||| | || ||||   |||| || |
gtaagtaaagaataatcacaatcttgtt-ttgctaatgactggtttaaccacctg---aatgtttaatgatgtttatg--------aaccagGATCTTGGTGGATCGCTAGGGAGAGACGCGGCTACTGGAAGAGGAGTGATGTTTGGTACCGAAGCTTTGCTTAACGAGCACGGAAAGACCATATCAGGGC

upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 6
--------gtaagtaat-tgtttgtttcatttcaatggccattgaag---tgaaatcaaatcatatgcttaatatatcattgcccttatgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC
        | |  |  | | ||    |||     |||   ||||  |   || | ||   |  | |   |||| |  || ||    ||  || ||| ||| |||||||| ||||||||||| || ||||| || ||||||||| | ||||| |||||||||||||||||  | ||| ||||  ||||||||||  |  | ||||
attctttggcatatcctatattgaaatcaccatgatgtatattgctgccttggattctgtttgtttctataatctgacagtga---taaattcttt-aaattagGATCTCGGTGGATCTCTGGGCAGAGATGCAGCTACAGGAAGGGGAGTACTCTTTGCAACAGAGGCCCTTCTTCATGAACATGGGAAGAGCATTGCCGGAC

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|7284551|gb|AW597139.1|AW597139
EST:     ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA                         GATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
genomic: ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATAgtaagtaatt ... ttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
EST: gi|192308765|gb|FG999790.1|FG999790
EST:     ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA                         GATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
genomic: ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATAgtaagtaatt ... ttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
EST: gi|12496130|gb|BG046909.1|BG046909
EST:     ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA                         GATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
genomic: ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATAgtaagtaatt ... ttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
EST: gi|26058522|gb|CA801436.1|CA801436
EST:     ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA                         GATCTTGGTGGATCTCTCGGTAGAGACGCGGTTACAGGACGAGGAGTCCTC
genomic: ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATAgtaagtaatt ... ttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC
EST: gi|208192091|gb|GD992389.1|GD992389
EST:     ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA                         GATCTTGGTGGATCTCTAGGTAGAGACGCGGCTACAGGACGGGGAGTCCTC
genomic: ATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATAgtaagtaatt ... ttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaaatcaaatcatatgcttaatatatcattgcccttatgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC
                 gcttaat  putative branch site (score: 4)
                                 cccttatgttttttc  putative PPT
             atatgcttaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaattgtttgtttcatttcaatggccattgaagtgaaatcaaatcatatgcttaatatatcattgcccttatgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA