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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccatttttacatgggaaattggaaaactttcgttcaacatggttggaacggttttccaaacacaccctcaatgattcaatgttaactctttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGGTCAGAGTGTACCCTG

Basic information

species Glycine max
transcript GLYMA01G05860.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G05860.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------------------ctccatttttacatgggaaattggaaaactttcgttcaacatggttggaacggttttccaaac-----acaccctcaa---tgattc----aatgttaactctttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGGTCAGAGTGTACCCTG
                                                                        | | | |   |||     ||| | | |   |  | | |  |  | |||      |||  |  |      || ||||||   ||||||     ||    ||  | | | ||||||||| ||||||||||| || ||||||||||| ||||||  ||| ||||||||||| ||  | || ||    ||||| ||||| |  ||  | |     |
gtaataccagatttccctaaaatttcttctcactgctgatatgcagcagttgcacgcagttactgtggtttccgctaatggcacagccataatggaatattctaagcttactagtgctggtttctgtttatatgctcttggcatcctcaaatttgattcctactatccggacgttgtattgcagATGTTCAAACTAGAAGATGTCGCAATGGGAATATGGATCAATGAGATGAAGAAGGATGGGTTGGATGTAAAGTATGAAAATGATGGGAGGATTTTGGTCG

upper sequence: GLYMA01G05860.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
--------ctccatttttacatgggaaattggaaaactttcgttcaacatggttggaacggttttccaaacacaccctcaatgattcaatgttaactctttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGGTCAGAGTGTACCCTG
        ||  |    ||  |    | ||    |  ||   | | ||   | || || | ||    ||||  ||| |   ||   |||       | | |   ||||||||| ||||||||||| || |||||||| || ||||| ||||| ||||||||||  ||  ||   || |  ||  | |  || |  ||| |  ||  ||
tacaatacctaaaaccctagcttttcatttcctgattttctctcctac-cagctgcaa-gattaggaaaactaaccatgtttg---caacccctggtttat---gcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
















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|192312704|gb|FK004392.1|FK004392
EST:     ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAG                         ATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAG
genomic: ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAGgtatataata ... tttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAG
EST: gi|11412343|gb|BF424354.1|BF424354
EST:     ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGGAG                         ATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTTG-CATGAA
genomic: ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAGgtatataata ... tttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCT-GACATGAA
EST: gi|193414393|gb|FK379199.1|FK379199
EST:     ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAG                         ATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAG
genomic: ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAGgtatataata ... tttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAG
EST: gi|192312705|gb|FK004393.1|FK004393
EST:     ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAG                         ATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAG
genomic: ATGATATCGCTAGGACGGTGTCCAAGAAATTCAGAGAGAACCATTTGAAGgtatataata ... tttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaacggttttccaaacacaccctcaatgattcaatgttaactctttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGGTCAGAGTGTACCCTG
                                    tgttaac  putative branch site (score: 2)
                                          ctctttct  CT-rich tract
                                  aatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccatttttacatgggaaattggaaaactttcgttcaacatggttggaacggttttccaaacacaccctcaatgattcaatgttaactctttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGGTCAGAGTGTACCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
ctccatt
- - - - - acatggg
- - - - - - - - - - - ggaaaac
- - - - - - - - - - - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt