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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtttttattacaattgtaacgaatgatctgttattgaaacttgaaagtttcttttctcatatctgataaaattatcttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCAATTTGCATTAGGACTCACCGATGGTGGAGTACATGTACTTGAACCACTA

Basic information

species Glycine max
transcript GLYMA17G12110.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 25
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 25
------------gtgcgtt-tttatta-caattgtaacgaatg--atctgttattgaaacttgaaagtttcttttct-catatctgataaaattatcttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCAATTTGCATTAGGACTCACCGATGGTGGAGTACATGTACTTGAACCACTA
             ||  || ||||  | | ||  | | ||||   || |    ||    | |      ||   ||||   ||||| || | |  || ||    ||||||||||||| | ||||| ||  |||| |||||||| || ||||| ||||| ||||||||||||||||| |||||||| ||    |||||||||||||||
gtgcctatttttctgaattatttacaaaccatgatgatgaataccattttccctttttccctattcactttccttctatgtatctaatgatacgatttt---gcagCTTGAGAGTGTACCCTCTCGTCGTTGCGGCACATCCATCTGAACCTAATCAGTTTGCATTAGGACTCACAGATGGTGGGGTGTGCGTACTTGAACCACTA
















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|17400966|gb|BM177748.1|BM177748
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|22926918|gb|BU544057.1|BU544057
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|16348877|gb|BI974472.1|BI974472
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCTAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|58018746|gb|CX705488.1|CX705488
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|6341823|gb|AW164647.1|AW164647
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|302141350|gb|HO212226.1|HO212226
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|7640283|gb|AW734588.1|AW734588
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|254332906|gb|GR850156.1|GR850156
EST:     AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: AGATTAAGATGTAGAATAAATCAATCTGCTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
EST: gi|13482451|gb|BG511794.1|BG511794
EST:     CTTATCTCCATCCCAACCCAAG                         CTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA
genomic: CTTATCTCCATCCCAACCCAAGgtgcgttttt ... cttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgaaacttgaaagtttcttttctcatatctgataaaattatcttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCAATTTGCATTAGGACTCACCGATGGTGGAGTACATGTACTTGAACCACTA
                              atctgat  putative branch site (score: 4)
                                         ttatctttt  putative PPT
                            atatctgataaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtttttattacaattgtaacgaatgatctgttattgaaacttgaaagtttcttttctcatatctgataaaattatcttttgacagCTTGAGAGTGCATCCTCTTGTGATTGCTGCACATCCCTCCGAACCCAATCAATTTGCATTAGGACTCACCGATGGTGGAGTACATGTACTTGAACCACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG