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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttttataatttcttgtttagagttaataaaatatttagtatttaactatttattgatgtacagttatgtattttaatattgcttgtgaaactttcagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT

Basic information

species Glycine max
transcript GLYMA06G13140.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 13
-------------------------------aatttttataatttct--tgtttagagt-taataaaatatttagtatttaactatttattgatgtacagttatgtattttaatat-----tgcttgtgaaacttt------cagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT
                                 || |  |  | |||  ||||   | | || ||  |   ||  | |  |  |  || |  ||| | |  | || | |  ||||      |  || || |  |||       ||||||| || || ||||| ||||| ||||| ||||||||  | |||||  ||||||| || || ||||||||||| || ||| |||||||||| |||||  
gttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattctactaccagcattgttgtcgatatgcttttaaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------------aatttttataatttct--tgtttagagt-taataaaatatttagtatttaactatttattgatgtacagttatgtattttaatat-----tgcttgtgaaacttt------cagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT
                                                                              || |  |  | |||  ||||   | | || ||  |   ||  | |  |  |  || |  ||| | |  | || | |  ||||      |  || || |  |||       ||||||| || || ||||| ||||| ||||| ||||||||  | |||||  ||||||| || || ||||||||||| || ||| |||||||||| |||||  
gcatgcctcttcaagttactttattttattttaagagagttaatagttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattctactaccagcattgttgtcgatatgcttttaaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 13
----------------------------------aatttttataatttcttgtttagagttaataaaatatt----tagtatttaactatttattgatgtacagttatgtattttaat--attgcttgtgaaactttcagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT
                                  | |    | ||      |  |||   ||| | ||  ||    |    | ||  |       | ||| | | |||||  || | |  ||| ||| ||      | |||||||||| || ||||| ||||| ||||| ||||||||  | |||||  |||||||||| || || ||||||||||| ||| | |||||||| |||||  
gcatgtttgtttttgttaacttacctttttggcaagtaaaaagaaaagagcgagtagtcctaacataaggttgccatgaagtctagattggagcagctgtgcggatatgtgattaatttcatttctt-tgtgttcattagCTTACTGCCTACCATGAAAGTGGACATGCTATTGTTGCACTCAACACCCAGGGTGCTCACCCCATACACAAGGCAACTATCCTTCCTCGTGGGTCTGCCC

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 13
-----aatttttataatttcttgtttagagttaataaaatatttagtatttaactatttattgatgtacagttatgtattttaatattgcttgtgaaactttcagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT
     ||||  ||  |  |||   || || |  ||     ||| ||    |  ||       | | |   ||| | | |  | |  ||||||       |||||||||||||| ||||||||||| || ||||||||||||||  | ||||| || |||||||| |||||||| ||||||||||| |||||||| ||||||||||
ctgtaaattgctactaactctgaatttgattagatc---cattcagagcct--ctgcaccacggtttttggttttttgtgcttactttgcttcatctcttttcagCTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGATGGTGCTCATCCAATTCATAAGGCAACAATTATGCCTCGGGGATCTGCTT

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|22523127|gb|BU081938.1|BU081938
EST:     TTATGGGTACAGAACGGAAAACAATGTCCATATCCGAAGAGTCAAAAAAG                         CTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAG
genomic: TTATGGGTACAGAACGGAAAACAATGTCCATATCCGAAGAGTCAAAAAAGgtaatgtaca ... aaactttcagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactatttattgatgtacagttatgtattttaatattgcttgtgaaactttcagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT
                            ttttaat  putative branch site (score: 3)
                                                ctttc  putative PPT
                tacagttatgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttttataatttcttgtttagagttaataaaatatttagtatttaactatttattgatgtacagttatgtattttaatattgcttgtgaaactttcagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT

- - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt