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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctaaattgtggttaaggtctgataagtttgaatacacccaacttttcttttggtttttaagatatatatggaagctaactcaatttccctcttgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATTTCCAGATGACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGG

Basic information

species Glycine max
transcript GLYMA03G22450.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22450.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 3'ss of exon 6
tagctaaattgtggttaaggtctgataagtttgaatacacccaacttttcttttggtttttaagatatatatggaagcta-actcaatttccctct---tgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATTTCCAGATGACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGG---
         | || ||||   ||| | | ||   | |    |     | | | |      | |    |  || || |  | ||  || |||  | |   ||||||||||| || ||| ||||  | |||||    || ||| | ||||| || || || ||||||||||||  |||||||||||| |||||||||||| | |||   
---tgttcctctgtttaaacactgttga-ttcatacattttctttcatacgtatctcccattaagagttcattgatgtcatacctaacttctatttgcatgtagGAATGGGCTCTCAACCCAAGCGAAACAG---ATATCTTTTCTTGAAACTTTACCGGATGACACCCAAATCTCTAGAGAAGAGAGAGCATTTCGCTTTTGGATA
















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|193554994|gb|FK511827.1|FK511827
EST:     TAATCTTGCCTTTGTTGCACATATTTTCCAGCACAG                         GAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATT
genomic: TAATCTTGCCTTTGTTGCACATATTTTCCAGCACAGgtgagaataa ... cctcttgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATT
EST: gi|208061735|gb|GD859659.1|GD859659
EST:     GGATCACCAAATCTTAATCTTGCCTTTGTTGCACATATTTTCCAGCACAG                         GAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATT
genomic: GGATCACCAAATCTTAATCTTGCCTTTGTTGCACATATTTTCCAGCACAGgtgagaataa ... cctcttgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATT
EST: gi|207778475|gb|GD749318.1|GD749318
EST:     GGATCACCAAATCTTAATCTTGCCTTTGTTGCACATATTTTCCAGCACAG                         GAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATT
genomic: GGATCACCAAATCTTAATCTTGCCTTTGTTGCACATATTTTCCAGCACAGgtgagaataa ... cctcttgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATT
EST: gi|193716779|gb|FK650739.1|FK650739
EST:     GGATCACCAAATCTTAATCTTGCCTTTGTTGCACATATTTTCCAGCACAG                         GAATGGACTTTCAGCCCAGAACAAAACAACAAATGTCTCTCCTTGAGACAT
genomic: GGATCACCAAATCTTAATCTTGCCTTTGTTGCACATATTTTCCAGCACAGgtgagaataa ... cctcttgtagGAATGGACTTTCAGCCCAGA-CAAAACAACAAATGTCTCTCCTTGAGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttttggtttttaagatatatatggaagctaactcaatttccctcttgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATTTCCAGATGACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGG
                              agctaac  putative branch site (score: 2)
                                    ctcaatttccctctt  CT-rich tract
     ttttggtttttaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctaaattgtggttaaggtctgataagtttgaatacacccaacttttcttttggtttttaagatatatatggaagctaactcaatttccctcttgtagGAATGGACTTTCAGCCCAGACAAAACAACAAATGTCTCTCCTTGAGACATTTCCAGATGACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - -tgtggtt
- - - - - - - - - - - - - - - - - -tacaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaact