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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcccttaattaagcagtttattcaaacaggccatgtatgttgttagcaacgtgtttttgaagaatccttgtttctcatgtttgaactgttcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAACGCGGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAAGCCAGCGATG

Basic information

species Glycine max
transcript GLYMA06G38160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
atcccttaattaagcagtttattcaaacaggccatgtatgttgttagcaacgtgtttttgaagaatccttgtttctcatgtttgaactgttcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAACGCGGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAAGCCAGCGATG
 |    ||    |     || ||     ||  | |||   |       |   | || |||  |  | ||     |  |     ||  | |  |||   |||| ||||||||||||||| | || |||||||| ||||| ||||||||||||   || || ||||| ||||| ||||| || ||  ||||||| || || |
gtaatatagaagatagtgttgtttttgtag--cttgttaatcaaggaaagacttttcttgctgtgtactcaagccata-----gagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG

upper sequence: GLYMA06G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g03160.t01 (Vitis vinifera), 3'ss of exon 4
atcccttaattaagcagtttattcaaacaggccatgtatgttgttagcaacgtgtttttg-aagaatccttgtttctcatgtttgaactgttcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAACGCGGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAAGCCAGCGATG
                  | |   ||| ||| | |     ||||||  ||    |    | |||    | |   | | ||  |||   | |     | |||||||| ||||| |||||| | ||||| |||||||| |||||||||||||||  |  ||| ||||| ||||| ||||| ||||| || ||||| || ||||
-----------------gtaagagaaaaaggacttaccctttgttaataattgatcgagggaagggggcataaatttgattgttggtttat---gatatagGTTGTCAGTGAGCCAAGCTTGACAAAGTCAGGTGTGTACTGGAGCTGGAACAAGAACTCAGCTTCATTTGAGAACCAGTTGTCTCAGGAAGCTAGTGATG
















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|17400220|gb|BM177002.1|BM177002
EST:     TAACCAAGGTTTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|7693171|gb|AW761268.1|AW761268
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCANGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|7692645|gb|AW760746.1|AW760746
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCANGANAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|192317174|gb|FK009775.1|FK009775
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|209720569|gb|BW677304.1|BW677304
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|6718926|gb|AW306573.1|AW306573
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|213589593|gb|DB982654.1|DB982654
EST:     CAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: CAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|192309153|gb|FG999086.1|FG999086
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAG-AAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTA-CAAAATCA
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCA
EST: gi|209722304|gb|BW665814.1|BW665814
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|6718485|gb|AW306132.1|AW306132
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|192307156|gb|FK002304.1|FK002304
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|209708857|gb|BW673893.1|BW673893
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|151399417|gb|EV269288.1|EV269288
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|12690020|gb|BG156356.1|BG156356
EST:     TAACCAAAGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAT                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|209726907|gb|BW675334.1|BW675334
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|192297785|gb|FG992803.1|FG992803
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCGAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|151401803|gb|EV271616.1|EV271616
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|298165448|gb|HO011497.1|HO011497
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|117557761|gb|EG702146.1|EG702146
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|8404324|gb|BE059958.1|BE059958
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|26059447|gb|CA802361.1|CA802361
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|192309154|gb|FG999087.1|FG999087
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|10256505|gb|BE824271.1|BE824271
EST:     TNNNCNAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|214006830|gb|DB987684.1|DB987684
EST:     CAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGGGCTGGAAC
genomic: CAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|5057756|gb|AI736232.1|AI736232
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|10255794|gb|BE823560.1|BE823560
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|9983406|gb|BE657514.1|BE657514
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|192297103|gb|FG988199.1|FG988199
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|14195748|gb|BE657567.2|BE657567
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|31471792|gb|CD413820.1|CD413820
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|7692208|gb|AW760321.1|AW760321
EST:     GATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: GATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|213597261|gb|DB981597.1|DB981597
EST:     AACCAAGGGCTTTGT-TGCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: AACCAAGGGCTTTGTCT-CAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
EST: gi|6483132|gb|AW202324.1|AW202324
EST:     TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAG                         GTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC
genomic: TAACCAAGGGCTTTGTCTCAGAAGATGAATCAGGAAAGAGACTTGCACAGgtaatatagc ... tcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaacgtgtttttgaagaatccttgtttctcatgtttgaactgttcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAACGCGGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAAGCCAGCGATG
                                         ctgttctt  CT-rich tract
         tttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcccttaattaagcagtttattcaaacaggccatgtatgttgttagcaacgtgtttttgaagaatccttgtttctcatgtttgaactgttcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAACGCGGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAAGCCAGCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- cccttaa
- - - - - - - - - - - tcaaaca
- - - - - - - - - - - - - - - -ccatgta
- - - - - - - - - - - - - - - - - - - tgttgtt