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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagtctctacattttattcgacaattacacatactggattttttgttcattaagtagtgagcttatggatctctgctttataga

Basic information

species Glycine max
transcript GLYMA18G03480.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 5
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagtctctacattttatt-cgacaattacacata---ctggat-tttttgttcattaagtagtgagcttatggatctctgctttataga
 | ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || || |||  ||  | |||  ||  | ||| |||| |      ||||  ||   || |||  | || ||  || |  ||                           
GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCGgtt-tgtcaaacttcatattgtatttcttttggtacaagtaggccttgatactattcttgtttgaacag---------------------------

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 6
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagtctctacattttattcgacaattacacatactggattttttgttcattaagtagtgagcttatggatctctgctttataga-
 | ||||| ||||| || || ||||| ||||| || ||||||||||||||||||||||||||||| || || |||  ||  | | |   | |  | || ||    || ||             ||||  |||   ||||    |  | ||     |    |||  | | 
GTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCGgtt-tgtgaacttgtgtacttcataaagcactt------------cttttccttc--caagtctaaatttgatattctttctatttggacag

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 5'ss of exon 5
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagtctctacattttat-tcgacaattacacatactg-gattttttgttcattaagtagtgagcttatggatctctgctttataga
 | ||||||||||| || |||||||| |||||||||||||| ||||||||||||||||||||||| || || |||| ||   | | |   |  |  |||   |  ||| |   | ||| ||  |||||||     | ||| |    | | |   || |     |  ||| 
GTTGCTGATTCACTTGAAAAAGGAACAGAACATGAAGATGAGTACATGATCAGTGAAAAGGAGCTTCTTGTTAACAGgtttatactgctccagctctttccataaacactctgagataatgtaatttttttaaggtcaagaaaactgataacaaatgtgaaagt-gtag-

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaa---tttca-----gtct-----ctacattttattcg--acaattacacat-actggattttttgttcattaagtagtgagcttatggatctctgctttataga
 ||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| || |||||||| || || | ||||   |||||     ||||      |||||| |    |  |||| ||   |  | || ||||| || | |||    ||| |        ||   || |||  || 
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcc-cagtcaatacgcctattcttggtttgcag-

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S303_47V6.1 (Physcomitrella patens), 5'ss of exon 5
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGta-atttcagtctctacattttattcgacaattac----acatactggattttttgttcattaagtagtgagcttatggatctctgctt-tataga---
 | || |||||  | || || || || |||||||||||||| |||||||||||||| |||||||| || || |||| |||  | |    || |     ||  | | |    |     |  |   | |||  |   ||| |  ||  || | | | | | |   |    |  |||   
GTGGCAGATTCTTTAGAAAAGGGCACGGAACATGAAGATGAGTACATGATCAGTGAGAAGGAGCTTCTTGTTAACAGgtatgtctttccctttttcccttgataggctgggatgtcgatgtttagaattgatgcctcaatttgttttgcgttaaggaaacgaagtgaatgcagattt

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S266_44V6.1 (Physcomitrella patens), 5'ss of exon 3
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaa----tttcagtctctacattttat-tcgacaattacacatactggattttttgttcattaag-tagtgagcttatggatctctgctttataga---
 | || |||||  | ||||| || || |||||||||||||||||||||||||| || ||||| || || |||||||||| |    ||   |||| |    | ||| ||  |   |    |     |   |   | || ||  | | | |  |||| |    | ||  |  | ||   
GTTGCGGATTCTTTAGAGAAGGGTACGGAACATGAAGATGAATACATGATCAGCGAGAAGGAACTGCTTGTAAACAAgttagtctttctcgtctttctcgtctatctcctcttctttgaaagagaggcatgccgatcgttgcgattgaggccttaagtcgttttgaatatttgaagc

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|298197159|gb|HO041902.1|HO041902
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|208197894|gb|GD998009.1|GD998009
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTNTATCCCAAAGGACATGGGAACGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTT
EST: gi|192302735|gb|FG993755.1|FG993755
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATAGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|208263408|gb|GE063318.1|GE063318
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTNTATCCCAAAGGACATGGGAACGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTT
EST: gi|208109910|gb|GD906228.1|GD906228
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTNTATCCCAAAGGACATGGGAACGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTT
EST: gi|5606114|gb|AI900212.1|AI900212
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|6725080|gb|AW309479.1|AW309479
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|254342930|gb|GR859092.1|GR859092
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|254334110|gb|GR849028.1|GR849028
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|192304323|gb|FG996449.1|FG996449
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|207786390|gb|GD757075.1|GD757075
EST:     ATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: ATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|208307666|gb|GE107610.1|GE107610
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|193445949|gb|FK413530.1|FK413530
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|21676489|gb|BQ628840.1|BQ628840
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|151411324|gb|EV281135.1|EV281135
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|31309603|gb|CD394806.1|CD394806
EST:     ACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACCAA-                         TTCATTTCTATCCCCAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: ACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAAC-AAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|192302734|gb|FG993754.1|FG993754
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATAGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|254342931|gb|GR859093.1|GR859093
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|192297468|gb|FG992696.1|FG992696
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|51334757|gb|CO978623.1|CO978623
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|254334109|gb|GR849027.1|GR849027
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|298178531|gb|HO024266.1|HO024266
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAAC
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAAC
EST: gi|298163034|gb|HO011767.1|HO011767
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|298176675|gb|HO026796.1|HO026796
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|208066461|gb|GD863124.1|GD863124
EST:     ATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: ATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|6567248|gb|AW234859.1|AW234859
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATNTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|192323071|gb|FK017012.1|FK017012
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
EST: gi|192304324|gb|FG996450.1|FG996450
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAA                         TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagt ... gctttatagaTTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaatttcagtctctacattttattcgacaattacacatactggattttttgttcattaagtagtgagcttatggatctctgctttataga

- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT