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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC

Basic information

species Glycine max
transcript GLYMA07G40230.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
--atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttg----acagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
  ||| ||| | || |  || |  | |  | |  || |     |   | |  |    || || |     || |    ||| ||  ||||||  ||||      ||||||||  | || || |||||||| ||||| ||||| |||||| ||||||| ||||| |||||| | ||||| || || ||||||||||| || |||||||
gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgtttt----ttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 25
atactttgtaatggctttttaatct------actagaaagatgcctttaacaaaatagaagatcttgtattactggag----gtgtctcatt--ttaatgaaat-------------tttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
     ||||    | ||||| | ||      |||       |  | | |  |  |||  | | |    ||||| |  |     | ||| ||   |  | ||| |              ||  ||||||||| | || ||||||||||||||||| ||||| || ||| |||| |||||||| |||||| | ||||| || || ||||||||||| || || ||  
--gtattgtctcagttttttgagctctcttaactgagggagttgcctcataattataataaaaccgacattacagttgcattatatcttatccatccaggaagtgacgatttcctttctttgcagCAAGAGTTAATCAGGACAGTTGATCTTGGGCCTTTCAAACATGTTGTAGATGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACTTTAT

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
--atactttgtaatggcttttta-atctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
  |   | |  | ||  |    | |  |  ||      | | | ||| | | |||||| | || | || |      ||   |||||      |  |||  ||| ||||  | || ||||| |||||||||||||| || |||||| |||||||||| || || ||  ||||||| || |||||||| |||||    ||  || 
gtaagttcttcagtgattcagcacagttgttatctgtgt-catataatacattagaaggttttatcttccatcgcctgagacattt------atcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 26
-atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
  | ||    |||   || ||  | | ||       |     ||      |    |||      | || |        ||  ||| |||    | || ||||||||| | || || ||||| |||||||||||||| |||||||||||||||||||| |||||  ||||||| || ||||||||||||||||||||| |||
tctgctactaaatttattgtttttatccttttccttttttgctattctttttattgataccaagtgacggttaaatattctgtttcatgtttctatg-cagCAAGAGTTAATTAGAACAGTCGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGTCTTGAGCTGAGGAAAGCAGCTTTTGAATGTGTAGACACACTGC

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: PP1S35_209V6.1 (Physcomitrella patens), 3'ss of exon 25
atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcatt---ttaatgaaattttg-------acagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
              || |||  | ||||       |||||||     |  | ||     |||  ||   |  ||   ||| |   ||| | |   || |         || |||||||||| ||||| || |||||||||||||| |||||||||||||||||||| || ||| | |||||||  || ||||||||||| || || ||||
----------tcttctgttttgtttactccgcgtctgccttttgttcagaacaacgatctgtggtatccgcagttgttcactaaattattcatcgttggtggatgtgtagAAAGAGCTCATCAGGACCGTGGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGGCTGGAACTCAGGAAGGGAGCCTTTGAATGTGTGGATACCTTGC

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: PP1S337_6V6.1 (Physcomitrella patens), 3'ss of exon 24
---atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
   || || | | |  | | | |  |   || |     ||||   |    | ||   | ||| |  |  |   | ||||   |  |   |    ||     || |||||||||| || || || |||||||| ||||| ||||||||||||||||||||||| ||| | || |||| ||||||||||||||| || || ||||
tttattctctatgactggtatgtgctaatcttggttattgccaggagttcactaatcgctctggcttgccaatatgtgttaaacgtgggttggttt---gtagAAAGAGCTCATCAGAACCGTGGATCTTGGACCTTTCAAGCATATTGTGGATGATGGACTAGAACTCAGAAAGGGGGCTTTTGAATGTGTGGATACCTTGC

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: EFJ37421 (Selaginella moellendorffii), 3'ss of exon 23
atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
                             | | |||   || |    | |  |  || || | ||               |||||||    |||||  || ||||||| ||||| ||||| ||||| |||||||| ||||||| |||||| || || || |||||||||||||  || || || || || ||||| ||||
-----------------------------gtacgatcttttcattggagtc-agcatgttatgtt---------------ttttaatctcgttttg-tagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGACGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
lower sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 23
atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
                             | | |||   || |    | |  |  || || | ||               |||||||    ||||| ||| ||||||| ||||| ||||| ||||| |||||||| ||||||| ||||||||| || || |||||||||||||  || || || || || ||||| ||||
-----------------------------gtacgatcttttcattggagtc-agcatgttatgtt---------------ttttaatctcgttttg-cagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC

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|208264078|gb|GE061230.1|GE061230
EST:     GGCTTCTTCCTGATCTGCTGCCTCTTCTATATGATCAAACTATTGTTAAG                         CAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGAT
genomic: GGCTTCTTCCTGATCTGCTGCCTCTTCTATATGATCAAACTATTGTTAAGgtaacctgaa ... attttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGAT
EST: gi|151410822|gb|EV280637.1|EV280637
EST:     GGCTTCTTCCTGATCTGCTGCCTCTTCTATATGATCAAACTATTGTTAAG                         CAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGAT
genomic: GGCTTCTTCCTGATCTGCTGCCTCTTCTATATGATCAAACTATTGTTAAGgtaacctgaa ... attttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGAT
EST: gi|20812570|gb|BQ297048.1|BQ297048
EST:     GGCTTCTTCCTGATCTGCTGCCTCTTCTATATGATCAAACTATTGTTAAG                         CAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGAT
genomic: GGCTTCTTCCTGATCTGCTGCCTCTTCTATATGATCAAACTATTGTTAAGgtaacctgaa ... attttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
                                   ttttaat  putative branch site (score: 3)
                                tcattttaatgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA