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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG

Basic information

species Glycine max
transcript GLYMA06G09320.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 6
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
                                              || | |  || ||  |  ||| |||| || | | || |||       ||   |       |||       | |||    |||| || ||||| || ||||||||||| |||||||| |||||||||||  | ||||| ||||| ||||||||||| ||||| |||   |||||||||||||
---------------------------------------------gtactttcttctttccagcacacttga-gtttggattttcttcatgctaatcgctaagattgatgttgaattgtttgcacagGTGATCGACAAGTCCTTTGGTTTTGACACTGCGGTGGAGGAGGCTCAGAGGGCCATCAATGCTGCTCATGTTGAGGCTGAGAGTGCAGAGAATGGCATTG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
                                       | ||   |  | ||  ||||| | |    ||   || |   ||||    |  | |  | |||  |  | ||  || |  | | |  |||| ||||||| ||| |||||||| || ||||| ||||||||||| |||||||| || ||||| |||||||| ||||||| |||    |||||||| || |
---------------------------------------gtaatgatctttttcacattatattgacattagggtatgaattat----ggtgtatatgcataatttgttt--ctaccctatgtgcagGTAATTGACAGATCATTTGGTTTCGACACTGCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaa---gtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
      |  || |  ||  || |   ||| ||  | |||| ||          | ||||| ||  | |||||    |      || ||||| ||  || | |   ||     ||     |    ||  ||||||| ||||| || ||||||||||||| ||| || || ||||| || ||||||||| |||||||||||||||| |||  ||||  ||||||||| || |
-----gtaatttatgattaca-agcgtttatttttgcctgcaaaga-------agcattacaactcttttgatactgcacaatttttctattaaagaagtactgattttttctgtacattaaaactc-agGTTATAGACAAGTCCTTTGGTTTTGATAGTGCTGTAGAAGAGGCCCAGCGTGCCATTGATGCAGCTCATGTTGAGGCTTCAAGTGCTGAGAATGGAATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggtt-atctatgaaga-aacttcatgttcggattgccttcttttt---ctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
||||  || ||     ||  || | | |  ||  |   | ||| |      || |  |    || |  || |  ||  |||| ||    ||  |  ||||  || |    || |||| || ||     |||| | |||||||| || |||||||||||||| || || || ||||| || ||||||||| || |||||||||| ||||||   |||  ||||||||| || |
gtatttttttt----gtgcgatgtgtct-atttttgtgtagaaat------ttgttgtacgcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgcct---tctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG------------------------------
                                                                                          |||    |  | | | ||||   |   | | | |  ||||||||| ||||| || ||||||||||||||||| || || || || || ||||||||||||||||||||||| ||||||  ||||  ||| ||||| || |                              
--------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttc--atgttcggattgcct---tctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
   |  || ||  | |  || || || || |   | |      |    ||  | |   |  |   |  ||||  ||   |       || ||| || |    | | | ||||   |   | | | |  ||||||||| ||||| || ||||||||||||||||| || || || || || ||||||||||||||||||||||| ||||||  ||||  ||| ||||| || |
--gtaatttttggccacttc-tacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatt-tgaagtgttggttatctatgaagaaacttcatgttcggattgccttct---ttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
                 || |||| |||   ||| |  |  |    || | |  |    |||||  |   |||  | |    |    |     |   |   ||  || | |  ||  |     |  || |||| |||||||| || |||||||| || || || |||||||||||||||||||| || ||||| |||||||| ||||||| ||||  ||||||||| || |
-----------------gtaatatgtttc--tccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G443985_T03 (Zea mays), 3'ss of exon 8
gtatgcttgttcacaatgtcatatttttt-gttcctccctggaactctaatcttatcatt-aaaatac-atttgaagtgttggttatctatgaagaaactt-catgttcggattgcc---ttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
                |   || ||| |       |   ||  | | |  | | |  ||  || || | ||||||  || |    ||  |  | ||| |    |||   | |||  |   | |   |  || |||| |||||||| || |||||||| || || || || ||||||||||||||||| || ||||| |||||||| || |||| ||||  ||||||||| || |
---------------gtaatatgtttctccacattttagtgacatttttgtgtaaaaatggaagatgccatttgacatgatcac-atgaacaacgaaccccatatgcgtgaattcaccgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
              ||| |  |      | |   | | |   | || ||     ||  || | |||      | | | ||  |   |||    ||  | |    |  ||        ||   ||||| | || ||||| ||||||||||||||||| || || || ||||| || ||||||||| || |||||||||| ||||||   |||  ||||||||| || |
------------gtaatattctgcaagatatgtttactttctattcaaaagccgtctctaca-taccccattaatat-ggccactcatgtg--aatgtgacacacaaatc-----tattgattttagATCATCGACAAGTCTTTTGGTTTTGATACGGCTGTGGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
              ||   |    || |  ||  |        ||  | ||| | | ||||  | | | |    |  ||||||  |   ||||| ||  || |   ||| |  |   | |  | ||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||||||    ||| | || || |||||||
------------gtaagtcctagattatcattattgt---agtctgcactctcaaccttaacctcc-tctcctattctggttagttcgcaagaagctcaatttgatgatag--tatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 8
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
   | ||| ||  | ||  ||  |   ||  |  |        ||| |   || ||| ||||   | ||    |  || |    || | | |   |||||   |  || |||||||| ||  || |||||||||||||||| ||||||||||||||||| ||||| || || || |||||||||||||| || ||||||||| ||||||||||||||||||| ||||
--gtacttcttgcctattgcacctgaattaattttgttcttttctccatctttttcaataaa---cctt----gcattagc---ctgtaatgtgtcttcac-cttagactgccttctcttgattcagGTTATTGACAAATCGTTTGGTTTTGATACTGCTGTTGAAGAAGCACAGCGTGCCATTAATGCGGCACATGTTGAATCTGAAAGTATTGAGAATGGTATTG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------gtatgct--tgttcacaatgtcatattttttgttcctccctggaactctaatcttatcat-taaaatacatttgaagtgttggttatctatgaagaaacttcatgttcg--gattgccttctttttctt--tagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
                                                                | | |||  | ||   |      | |         || || |      | || | || || ||   |    |||||||    ||   | |      || | ||| || |  || ||   | |||    |   |||| || || || || || || |||||||| || || || || ||||| ||||| || |||||||||||||| |||||||| ||| || |||||||  |||
gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgat-taattatgtattgttttcttgaagtccaagtgtgccaccgtctaa-tgcatatttgtcgaatgtggtatttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatt---tgaagtgttggttatctatgaagaaacttcatgttcggattgcc-------ttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
||| | || |  |||    |  |  ||      | |  ||||| |||    || ||| |  | |  |||   ||   |  || || |   | ||| |||   |     | || |         | |   ||    |||| || |||||||| |||||||||||||| || ||||| || || || ||||| |||||||| || || || |||||||| ||| || | ||||||||||
gtacgttt-tagaca----cggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG

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|193721856|gb|FK659432.1|FK659432
EST:     TGAAAGTAGCAATTGCTGGAATTCCTAAAACCATAGACAATGACATCCCG                         GTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGT
genomic: TGAAAGTAGCAATTGCTGGAATTCCTAAAACCATAGACAATGACATCCCGgtatgcttgt ... ttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGT
EST: gi|207822613|gb|GD795682.1|GD795682
EST:     TGAAAGTAGCAATTGCTGGAATTCCTAAAACCATAGACAATGACATCCCG                         GTTATTGACAAATCTTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACG
genomic: TGAAAGTAGCAATTGCTGGAATTCCTAAAACCATAGACAATGACATCCCGgtatgcttgt ... ttttctttagGTTATTGACAAATCTTTT-GGTTTTGATACTGCGGTTGAGGAGGCTCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
                                    ttgccttctttttctt  CT-rich tract
                                            tttttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA