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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaaaaaatataattcttgtgaaaaggtacaatggtagagggacagtaaaaacatcaaattatctttttctgagttatagatttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

Basic information

species Glycine max
transcript GLYMA08G08330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------cttaaaaaatataattcttgtgaaaaggtacaatggtagagggaca----gtaaaaacatcaaattatctttttctgagttatagattt--ggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA
                                                                             |||  |||   |      ||    |||     ||  |  ||     |    |   || | | |  ||  |      || | || |  ||   |  |||  |||| || ||| | ||||||||||||||||||||| |||||||| | |  || ||||| || ||||||||| | ||||| ||||| || || ||||| || |
gtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggattcccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctatggaagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATTCTGCTTGGAGCGCGGCAGTATTCCACACCAGTTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAA

upper sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
cttaaaaaatataattcttgtgaaaaggtacaatggtagagggaca-gtaaaaacatcaaattatctttttctgagttataga---tttggcgattgtt--tgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA
    |  ||  || |||    || |  ||| |||  |  |  |  |  |  | |  ||| ||    |  |  | | | | | |   ||||   ||||||  | ||||| || || || |||||| |||| ||||| ||  | || ||||| |||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||
----agtaagctagttc--aagatactgtaaaatatttcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA

upper sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
cttaaaaaatataattcttgtgaaaaggtacaatggtagagggacagtaaaaacatcaaattatctttttctgagttatagat-ttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA
 |      | | |   | | |||  |  |    ||||  |      |  |  |  ||  |||||  | |   |  | ||| |  |||| | || |    ||||||| || |||||||||||||| || |||||  |||||||||| |  || |||||||| || |||||| | ||||| ||||| || |||||||| ||||
-tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA

upper sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
-cttaaaaaatataattcttgtgaaaaggtacaatggtagagggacagtaaaaacatcaaattatctttttctgagttatag-atttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA
  |   |  ||  || | |||| |   | ||   |  | |    | |   |   |||     |     ||  || |||  |   | ||||  ||   || ||||||||||| ||||||||||||| ||||||||| |  | || || |  || || ||||| || || ||| | ||||| || |||||||| || || ||||
gatcttacgattcaaatgttgttagctgataacttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggc--ttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA

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|120531799|gb|EH259932.1|EH259932
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|192318183|gb|FK007213.1|FK007213
EST:     TAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|31307986|gb|CD393189.1|CD393189
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|192318154|gb|FK007212.1|FK007212
EST:     TAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|120531893|gb|EH260026.1|EH260026
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|11411903|gb|BF423914.1|BF423914
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|120531742|gb|EH259875.1|EH259875
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|18038935|gb|BM307229.1|BM307229
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|13790009|gb|BG652600.1|BG652600
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAG                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
EST: gi|7684881|gb|AW755529.1|AW755529
EST:     TTGGATTGGGTAGGGCTTTTGGAATTGCTGTTAAGACATATACACATGAG                         GTGGGGACACTGTGGTACAGAGCT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCT
EST: gi|11688056|gb|BF595732.1|BF595732
EST:     TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAC                         GTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT
genomic: TTGGATTGGCTAGGGCTTTTGGAATTCCTGTTAGGACATTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaaaacatcaaattatctttttctgagttatagatttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA
         atcaaattatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaaaaaatataattcttgtgaaaaggtacaatggtagagggacagtaaaaacatcaaattatctttttctgagttatagatttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

- -aaaaaat
- - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - aaaaaca