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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatagcaaatagttctagttttggttatgttttcatgatggatggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG

Basic information

species Glycine max
transcript GLYMA05G02260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G02260.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
----atcatagcaaatagttctagttttggttatgttttcatgatggatggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG
     |        ||      ||| |   ||| |   |||  |   |||  |     ||   | ||| || |      |||| ||    |  |  |  |||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||||||||| |||||||| || || || |||||  |  | |||
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgtt---cctaaggatataag-ttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG

upper sequence: GLYMA05G02260.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
atcatagcaaatagttctagttttggttatgttttcatgatggatggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG
                           ||  ||||| |  ||   || | |  || |  | || |   |||               |   |     ||||||| || || |||||||| || || || ||||| ||||||||||||||||||||||| || ||||| |||||||| ||  | ||||| || || || |||
--------------------------gtaacttttcttcttgagaggatttc-tccgaggctaagctctctcctc-----------tttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG

upper sequence: GLYMA05G02260.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35746 (Selaginella moellendorffii), 3'ss of exon 2
atcatagcaaatagttctagttttggttatgttttcatgatggatggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG
                         || || |||        || | || |  || |  | || |      | ||    |      |   |     ||||||| || || |||||||| || || || ||||| ||||||||||||||||||||||| || ||||| |||||||| ||  | ||||| || || || |||
-------------------------gtaatttttcttcttgagaggatttt--tccgaggctaag-----ctcattcctc------tttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTACCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCCAAG

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|19934966|gb|BQ079996.1|BQ079996
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|6847194|gb|AW349484.1|AW349484
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|16277842|gb|BI942592.1|BI942592
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAGATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|298189417|gb|HO037820.1|HO037820
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|23057559|gb|BU578233.1|BU578233
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|58017948|gb|CX704690.1|CX704690
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|37996052|gb|CF807641.1|CF807641
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|298171533|gb|HO016565.1|HO016565
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|31467330|gb|CD409358.1|CD409358
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
EST: gi|20449672|gb|BQ253796.1|BQ253796
EST:     GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATAC                         TGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatgc ... tgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG
                       tcttgat  putative branch site (score: 4)
                                    aataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatagcaaatagttctagttttggttatgttttcatgatggatggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - ggttatg
- - - - - - - - - - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - - tggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgtgg