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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT

Basic information

species Glycine max
transcript GLYMA05G03270.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatc--tcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
 | ||       || | |||||| |  |  || |  || ||| |  ||| |   ||  |||      |   | |||  ||  || |   |   ||||  ||||||| || |||||||| || |||||||| || ||||||||||| || || ||||| ||||| ||| | || |  ||||||| ||| |||||||||||||| |
-atttggctttcctca-ataattcttctctcc-taaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtcttt-atgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatctcaactttgaattaccttt-tgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
 | ||       || | | |||||  ||  || | ||| ||     ||| |   ||  |||      |   | |||       |    ||| | | |   ||||| || || ||||| || |||||||| ||  |||||||||| || || ||||| ||||||||| | || || ||||||||||| ||| |||||||||| |
aatttggctttcctcaaaaaattt--atctcc-tataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT

upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
caattaataaatct-aatata--attttgatgaccatctaac-ttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
|| || || |  || || | |  | ||  |  || |||     ||| |||||    || | |  || |       |||| |   |  ||||      ||||||||| ||||| || || ||  ||||||| ||||||||||| || || |||||||| || |||||  | ||||||||||||||||||||||||||||| ||||
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgc--aattgtgttctaaggaacaatcttagtgt--aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtg-cagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
                                             | | |     | ||||    | | ||   |   ||   ||  |  || | || ||||| || |  ||  | || ||||||||||| || ||||||||||| || ||||| || |||||  | ||||| || ||||||||||| |||||||| ||||
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtct---aacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
                                             | | |     | ||||    | | ||   |    | | |   | || |   |||||| || |  ||  | || ||||||||||| || ||||||||||| || ||||| || |||||  | ||||| || ||||||||||| |||||||| ||||
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttg--tctaacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|17022161|gb|BM093195.1|BM093195
EST:     TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgtttcatttc ... ttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|27425980|gb|CA937500.1|CA937500
EST:     TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgtttcatttc ... ttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|192328312|gb|FK020023.1|FK020023
EST:     TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgtttcatttc ... ttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|193435526|gb|FK401958.1|FK401958
EST:     TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCGTGCAAAGGAATCCTAATTATTTGGTCCCCCTGGAAC
genomic: TGCTTCCTTTACAGAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgtttcatttc ... ttttgtgcagCCGTGCAAAGGAATCCTA-TTATTTGGTCCCCCTGGAAC
EST: gi|26048337|gb|CA784840.1|CA784840
EST:     AAGGGGCAATTAACCAAG                         CCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: AAGGGGCAATTAACCAAGgtttcatttc ... ttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcaaaatattatccattctgttatctcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
                                        ttacctttt  CT-rich tract
      aaaatattatccatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - ccatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattct