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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattactatctttactgcttttttttttttttcattttaaatgctattatttttaatttgtgtcatattttctcttgggggtatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA

Basic information

species Glycine max
transcript GLYMA03G39290.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 22
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 21
gtgattac---tatctttactgcttttttttttttttcattttaaatgctattat----ttttaatttgtgtcatattttctcttgggggtatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA
 |   | |   ||| |||     |||  ||||    ||| |   |||| |    |     | ||       ||  |   |  | |   |   ||    |||| ||||| ||  | |||||||| || || || || || ||  |||| ||||| ||    || |||||| |||||||||||||||||||||| || 
atagcttcacatatgttttacagtttaattttcccctcactgctaatgttgccttaaaactctatcaacgatctgaaacttgcatattgtgttccatcagGTCAAATCAAAGCTAAAGGGTCACCAGAAACGCATCACAGGCCTAGCATTTTCTACAGCCCTCAACATCTTGGTTTCATCTGGTGCTGATGCACAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 21
gtgattactatctttactgcttttttttttttttcattttaaatgctattatttttaatttgtgtcatattttctcttgggggtatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA
|| ||||| ||  | ||    ||    | || |  ||  |   || ||    | |||| |  ||   |  | | |  ||       ||||||||| ||||| ||| ||||||| || ||||| ||  | ||||||||||| ||||| ||| |||| ||||||||||| |||||||||||||||||||| 
gtaattac-atgataacattgttcaagtcttatcaatggtttgtg-tagccctattaactgatgc--tgatgtttgctg-------cttctagGTAAAATCAAAACTGAAGGGACACCAAAAACGCGTAACTGGTTTAGCTTTTTCCACCAGTCTAAACATCCTGGTCTCATCTGGTGCTGATGCTCAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 22
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 21
--------------------------------------gtgattactatctttactgcttttttttttttttcattttaaatgcta--ttatttttaatttgtgtcatattttctcttgggggtatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA
                                      ||||||  |  |  |  || |  |   | | | ||  ||| |||   |   | |  || ||  |  | |||   | |||  |  ||   |   ||||||||   || |||||||||||||||||| |||||||||| ||||| || || | |  ||| ||  | || || ||||| || || |||||||| 
gtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgt---tcacagGTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTCTCTAACACTCTCAATGTTCTTGTATCATCCGGAGCGGATGCTCAG

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|163917881|gb|EH039022.1|EH039022
EST:     TTGGGATGGAGGACTCAACAATTCACATATACAATGTTAGAGTGGATGAG                         GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTT
genomic: TTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAGgtgattacta ... tatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTT
EST: gi|254343985|gb|GR857741.1|GR857741
EST:     TTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAG                         GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTT
genomic: TTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAGgtgattacta ... tatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTT
EST: gi|193540955|gb|FK496089.1|FK496089
EST:     TTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAG                         GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTT
genomic: TTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAGgtgattacta ... tatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTT
EST: gi|22522387|gb|BU081198.1|BU081198
EST:     TTGGGATGGAGGACTCAACAATTCACATATACAATGTTAGAGTGGATGAG                         GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGT
genomic: TTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAGgtgattacta ... tatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatgctattatttttaatttgtgtcatattttctcttgggggtatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA
              ttttaat  putative branch site (score: 3)
                                             tatcttct  putative PPT
        tattatttttaatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattactatctttactgcttttttttttttttcattttaaatgctattatttttaatttgtgtcatattttctcttgggggtatcttctagGTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT