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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcactcgtcacatttgcatgctaatagaatcaagtgtcagatgtcagtcagagacacataaaataaaatgtttgtattattgaaatattagaagcctttggtgtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT

Basic information

species Glycine max
transcript GLYMA03G37450.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 18
gtatcactcgtcacatttgcatgctaatagaatcaagtgtcagatgtcagtcagagacacataaaataaaatgtttgtattattgaaatattagaagcctttggtgtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT
                                             || ||| |  || |     | ||  ||  |  |  ||||    |  |      |||   |       ||||| ||||| ||||| ||||| ||    ||||||||||||||||| |||||||||||||| || |  ||| ||
---------------------------------------------gttagttatggataatagcattatgatcatcattgtatttgtgtgctcatgttcttccttt------cagGTGAATGGCAATCTAGTTTCACCAATCCATGTACTTGCAAATGCTGAAGTTGTGGAGATTATAATTTATGAT

upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 17
gtatcactcgtcacatttgcatgctaatagaatcaagtgtcagatgtcagtcagagacacataaaataaaatgtttgtattattgaaatattagaagcctttggtgtaaat--gcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT
           ||||||    |   || | |  | | |     || |   | | |    |  ||||| ||  |     |  |  |     ||||     |    ||    |  |||||| ||||| ||||| ||||| ||   |||||||||||||||||| ||||| |||||||| || || ||| ||
-----------cacattc---taaaaaaatagcctactccattatttatattacaattcctcaaaatgaaggg---aaacaaacggggccttagtgttttcatatgctcttttgcagGTGAATGGCAATCTGGTTTCACCAATTCATGTACTTGCAAATGCTGAAGTGGTGGAGATTATAACTTATGAT

upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 18
gtatcactcgtcacatttgcatgctaatagaatcaagtgtcagatgtcagtcagagacacataaaataaaatgtttgtattattgaaatattagaagcctttggtgtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT
||||  ||  |||| ||||   | ||  | | ||     ||| || | |||        ||   || ||       | |  || | |  |  | | || |||  |||   ||||||||||||| |||||||||||||||   ||||||||||| ||||| || |||||||||||||| || ||||| 
gtatt-cttctcacttttgaccggtataatattctttcttcatatctgagt-gtttctccaggcaaaaaggcaaaagaaggatagtatcaccacatgctttttttgt---tgcagGTCAATGGGAATCTTGTTTCTCCCATGCATGTACTTGCTAATGCTGAGGTTGTGGAGATAATTACCTATAAC

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|151406442|gb|EV276257.1|EV276257
EST:     ACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAG                         GTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTT
genomic: ACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAGgtatcactcg ... gtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTT
EST: gi|120496652|gb|EH224819.1|EH224819
EST:     ACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAG                         GTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTT
genomic: ACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAGgtatcactcg ... gtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTT
EST: gi|151402145|gb|EV271958.1|EV271958
EST:     ACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAG                         GTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTT
genomic: ACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAGgtatcactcg ... gtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaataaaatgtttgtattattgaaatattagaagcctttggtgtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT
     ataaaatgtttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcactcgtcacatttgcatgctaatagaatcaagtgtcagatgtcagtcagagacacataaaataaaatgtttgtattattgaaatattagaagcctttggtgtaaatgcagGTCAATGGAAATCTTGTTTCTCCCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT