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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtaagcttctgatgttgtatgttggtcactcctctgcccctttcacttacagggacagtattttgtatattgttaggttctataatttccttgaccctgctacaattttttaactaatgctctgatgaaatgaaatatcctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATGATGTACTATGGCTTGGTTATAGAAG

Basic information

species Glycine max
transcript GLYMA20G34920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01420.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtaagcttctgatgttgtatgttggtcactcctctgcccctttcacttacagggacagtattttgtatattgttaggttctataatttccttgaccctgctacaattttttaactaatgctctgatgaaatgaaatatcctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATGATGTACTATGGCTTGGTTATAGAAG
     || |    ||  | |      |||   |  |||  ||   |    ||||  ||  |    |  ||| | ||  ||   | | |          | | || |   |||| ||    ||     |||  | || || | |  |||| ||||||| |  | |||||  | ||   ||| || ||||||||| | ||||||||||||||||||||||||||  | ||||
-----gtgaatcccttttatatggatttga--aagccttagcatataaatcttatgggccc---ttgatgtgtgtttctaatatttgtctccatgaaaaacttgtttgtatttattttgaaaa----tgac-agatcaattgttttgtt-ttagGTGGTGTTGGAACAATTGACTTCTTCTCCCTGGAACAACATGTTTTTCATGATGTACTATGGCTTGGTAGTTGAAG
















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|192311022|gb|FK004725.1|FK004725
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACNNNNNNNNCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|31470211|gb|CD412359.1|CD412359
EST:     TAAAATCTTAAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTGTTCATG
genomic: TAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|23735013|gb|BU765769.1|BU765769
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTGTTCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|254316036|gb|GR825845.1|GR825845
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACNNNNNNNNCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|192311021|gb|FK004724.1|FK004724
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACNNNNNNNNCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|254323831|gb|GR840364.1|GR840364
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACNNNNNNNNCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|254316037|gb|GR825846.1|GR825846
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACNNNNNNNNCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG
EST: gi|254321581|gb|GR824898.1|GR824898
EST:     TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAG                         GTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACNNNNNNNNCATG
genomic: TGGATAAAATCTTTAAGGGGAACAAAGGCAATGATACTGTTGCTAAGAAGgtatggtaag ... ctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgctacaattttttaactaatgctctgatgaaatgaaatatcctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATGATGTACTATGGCTTGGTTATAGAAG
                                           tcctgtt  CT-rich tract
      tacaattttttaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtaagcttctgatgttgtatgttggtcactcctctgcccctttcacttacagggacagtattttgtatattgttaggttctataatttccttgaccctgctacaattttttaactaatgctctgatgaaatgaaatatcctgttattagGTGATCCTTGAACAGATAACCAGTTCCCCATGGAACAACTTTTTTTTCATGATGTACTATGGCTTGGTTATAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA