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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaactaaagagcaatcacattttgtgtgcattcttcatctgatgtttggagagcatattttcttgtgtttgaattcctctttctgatctatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGAAAAACCAACCATGGGGACCTAAGAAAATATTTATCTGGGTTTTTTGACA

Basic information

species Glycine max
transcript GLYMA12G35390.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
atgaactaaagagcaatcacattttgtgtgcattcttcatctgatgtttggagagcatattttc---ttgtgtttg------aattcctctttctgatctatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGAAAAACCAACCATGGGGACCTAAGAAAATATTTATCTGGGTTTTTTGACA
     |||||      | | ||  |||     ||  | || ||||| |   ||  ||| ||||    || |||| |      ||   | ||   || ||  |  ||||||| ||||||||||||||||||||||| ||||||||||||||  |||||||| | || ||| |||||||||||||||||||||||| ||| ||||| ||||
----gctaaacg----ttagatgctgttctgtttgattatttgatggt-aaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
















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|31462181|gb|CD404209.1|CD404209
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|8827856|gb|BE211586.1|BE211586
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|19269465|gb|BM885721.1|BM885721
EST:     TTGATGATGTACCATAAGCTCTACAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|15199320|gb|BI423772.1|BI423772
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|12689440|gb|BG155837.1|BG155837
EST:     TGATGATGCTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TGATGATG-TACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|58018251|gb|CX704993.1|CX704993
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|16342399|gb|BI967994.1|BI967994
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|22522469|gb|BU081280.1|BU081280
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
EST: gi|11274034|gb|BF324402.1|BF324402
EST:     TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAG                         GTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA
genomic: TTGATGATGTACCAGAAGCTCTAGAAAAGTGGCACACCTTGGGTATAAAGgttgttttca ... tatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggagagcatattttcttgtgtttgaattcctctttctgatctatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGAAAAACCAACCATGGGGACCTAAGAAAATATTTATCTGGGTTTTTTGACA
                                     ttctgat  putative branch site (score: 3)
                              ttcctctttctgatct  CT-rich tract
           atattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaactaaagagcaatcacattttgtgtgcattcttcatctgatgtttggagagcatattttcttgtgtttgaattcctctttctgatctatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGAAAAACCAACCATGGGGACCTAAGAAAATATTTATCTGGGTTTTTTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - -caatcac
- - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - -tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - tggagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg