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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagataaggcctatcagacatgttctcctagtggttgaatcgcttccagttttcatacttccacatgtatacagGTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACAAGTGAAGTCAGTGTTTCCTTGACATTGGATCCATCAAAGCTATGGAGCA

Basic information

species Glycine max
transcript GLYMA16G26300.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26300.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0244g00140.t01 (Vitis vinifera), 3'ss of exon 10
gtgagagataa-----ggcctatcagacatgttctcctagtggt-----tgaatcgcttccagttttcatac---ttccacatgtatacagGTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACAAGTGAAGTCAGTGTTTCCTTGACATTGGATCCATCAAAGCTATGGAGCA
||||||  |        |  | |    |    |||| |  ||       | |||     |   | | | ||    | |   ||  || ||||| ||||| ||||||||||| || || ||||| || |||||||| ||||| |||||||||||| | || ||||| |||||||||||||| || |||||| 
gtgagaattgctttgtagtttttgttgctccctctcttgttgccacatataaattctaactgctgtccgtatggttgctttatccatgcagGTTTTTTCTATCTTTGAAGATTTGGGTATATCTGTGGATGTTGTTGCTACCAGTGAAGTCAGTATATCTTTGACTTTGGATCCATCAAAACTTTGGAGCC
















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|208245175|gb|GE041583.1|GE041583
EST:     TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAG                         GTGTTTTCAATCTTTGAAGAGTTAGG
genomic: TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAGgtgagagata ... atgtatacagGTGTTTTCAATCTTTGAAGAGTTAGG
EST: gi|208096619|gb|GD893334.1|GD893334
EST:     TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTT-CCT-GCTAAG                         GTGTTTTCAAT
genomic: TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAGgtgagagata ... atgtatacagGTGTTTTCAAT
EST: gi|9986794|gb|BE660902.1|BE660902
EST:     TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAG                         GTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACA
genomic: TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAGgtgagagata ... atgtatacagGTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACA
EST: gi|58021976|gb|CX708717.1|CX708717
EST:     TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAG                         GTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACA
genomic: TGGATATAGTGAGTACTCGCATGCTTGGTCAGTATGGTTTCCTTGCTAAGgtgagagata ... atgtatacagGTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctcctagtggttgaatcgcttccagttttcatacttccacatgtatacagGTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACAAGTGAAGTCAGTGTTTCCTTGACATTGGATCCATCAAAGCTATGGAGCA
                              ttttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagataaggcctatcagacatgttctcctagtggttgaatcgcttccagttttcatacttccacatgtatacagGTGTTTTCAATCTTTGAAGAGTTAGGCATATCAGTTGATGTTGTAGCTACAAGTGAAGTCAGTGTTTCCTTGACATTGGATCCATCAAAGCTATGGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA