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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC

Basic information

species Glycine max
transcript GLYMA06G11430.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
gtattctactattc---ccttttcttatttttttgctct---cataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
||| |  || |  |    |||     |      ||| |    || | ||| |   |   ||    | | || |  ||| || | | |||  ||| | |   ||||||||||||||||||||| || || || |||||||| ||||||||||| ||||| ||||||||  | ||||| ||| |  | ||||||||  |   |||
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgc-agCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g36500.1 (Oryza sativa), 3'ss of exon 1
gtattctactattcccttttcttatttttttgc-tctcataaattctaatagactt-tgattataaaataatgttttctctgttt--caatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
      ||   |    ||  | |   |   ||| |   | | ||| ||     |||  || |||  |   ||  |  |||  |    ||| |  |  | ||| ||||||||||||||||| || || ||||||||||| ||| | ||||| ||||| ||  ||||  | ||||| |||||| |||||||||||      ||
-----gtaacgtatatttaccatgcgtgcatgcgtaaaacacattttaccgttcttgcgaatatgtatgtatactgactcgatcgaacaaatgctcatcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACGTGAACTCGGTGATCACGGCGCCCGGGCACGACGAGATCCTGCCCATCAACGGCATCAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 1
-----gtattctactattcccttttcttatttttttgctctcataaattctaata-gactttgattata--aaataatgtttt--ctctgttt--caatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
     ||||| ||| ||||  |  |     | |    | |   | |    | ||  || | ||  | ||   | |   ||| |  |||  |    ||| |  |  | ||| |||||||||||||| || || || ||||||||||| ||| | ||||| ||||| || |||||  | ||||| |||||| |||||||||||      ||
gtaacgtatt-taccattcattcatgcatgtgtaaaacacattttaccgttcatgcgaatatgtatgtactgagttgagttctgactcgatcgaacaaatgctcatcagCGTGGTGGTACAAGCCAGAGTACATCATCAACGAGCTGAACGTGAACTCGGTGATCACGACGCCCGGGCACGACGAGATCCTGCCCATCAACGGCATCAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 1
gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttt-tagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
||| |   |  |||   |||   | ||| || ||       | || |  | |     |  || |  |  ||  ||  || || ||| |  ||    ||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||| |||||  | ||||| |||||| |||||||||||      ||
gtaattagcagttcatgttt---aatttattact-------actcaagcaaa----aaaaatgatgtc-tgactttgctattgcaaatgattgagcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACATAAACTCGGTGATAACGACGCCGGGGCACGACGAGATCCTGCCCATCAACAGCATTAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G076723_T01 (Zea mays), 3'ss of exon 1
gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
|||  ||| | ||   || | |   |||  | |       ||    |  |  |       |    ||  || | |  ||| | |||  |      ||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||| |||||  | ||||| |||||| |||||||||||      ||
gtaa-ctagtgtttgtttgtttg--tttactacggatcggaagcaaagcaagcaagcgaaacgggattttgatcttgctgctgcaaaatgagc--agCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACATAAACTCGGTGATAACGACGCCGGGGCACGACGAGATCCTGCCCATCAACGGCATCAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G37130.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------------------------------------gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
                                                                                                  |  ||         | |     |     |  |  ||  |   ||  | ||    | | ||||  |    |    |    |||| |||||| ||||||||| ||||| || || || ||||||||||| ||||||||||||||||| || ||||| || |||||||||||  | ||||||||| | |  ||
gtacataaaatctttttgcttcaataaatctcattaagatgaactaattgatatgtttaaaaagtctccgaacctataggagaaaaacaaaaacagaaatcatattaaaaaatgaaaaactaatgttggtggatgatgtcagcttctgtgacttacataaattcaaattcaat--ggttttgttttagGTTGGTGGTATAAGCCAGAGTACATAATCAACGAGCTAAACATAAACTCCGTGATTACGACGCCATGTCACGAGGAGATTCTTCCCATCAACGCTTTCAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
         ||  |  ||  ||||   || |  |||  || ||| || |   |  || |     |||| | ||| || |||||     || ||  |||||||||||| ||||| || || || |||||||||||||| |||||||| ||||| || || ||| | ||||  ||||| || || || ||  |||  ||
--------gtaaactattaacttacccttgtcttcttttacattttagttaccgatgct-----aatattatttact-tgttt-----ttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC

upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gtattctac-tattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
                                  || |  || |    |  | | || | |||||| | | ||||||      |||    |||  | |  |||||||     | |        |     |||||||||||| |||||||| || || || || ||||| ||||| |||||||| || || || || |||||||| || ||||| ||||||||||| |||||
gtacactgcgccccacatccccccacccccctattaatagacatgactctctatattttgtttttggttttataaatgggcgaagatgaggatc-tgaggtaatgttactattttggttgacatggagcagCTTGGTGGTATAAGCCGGAGTACATCATTAATGAGCTGAACATTAACTCCGTCATCACTACACCATGCCACGAAGAAATCTTACCCATCAACTCCTGGAC

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|22540361|gb|BU090204.1|BU090204
EST:     TAACAGGGTACTCCCTTCTCACGTTGATGCCGAACTTGCCAATGCTCAAG                         CTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCG
genomic: TAACAGGGTACTCCCTTCTCACGTTGATGCCGAACTTGCCAATGCTCAAGgtattctact ... ttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCG
EST: gi|10846695|gb|BF069531.1|BF069531
EST:     TAACAGGGTACTCCCTTCTCACGTTGATGCCGAACTTGCCAATGCTCAAG                         CTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCG
genomic: TAACAGGGTACTCCCTTCTCACGTTGATGCCGAACTTGCCAATGCTCAAGgtattctact ... ttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCG
EST: gi|26057779|gb|CA800693.1|CA800693
EST:     TAACAGGGTACTCCCTTCTCACGTTGATGCCGAACTTGCCAATGCTCAAG                         CTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCG
genomic: TAACAGGGTACTCCCTTCTCACGTTGATGCCGAACTTGCCAATGCTCAAGgtattctact ... ttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC
                             ttttctctgtttcaat  CT-rich tract
               attataaaataatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA