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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtacaagttttcacggagaaattgttattttattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT

Basic information

species Glycine max
transcript GLYMA02G00680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g43540.1 (Oryza sativa), 3'ss of exon 3
--gttggtacaagttttcacggagaaattgttattttattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
  | ||  || | | |||    |  || | || ||  | ||  |   |    ||||    ||    |    | || |||  |||||||| |||||||  |||||||| || || ||||| |  ||||||||||| ||||||||||| |||||||| || |||||||| ||||||||| | |||||
gtgatga-accattcttcggctatgaactttttttccactgttaa-gtgcagtttta---attgaatgccatcctgatt--acagATGTGAAGAACAAGTGGGAGAACAGCTCATGGGGTAAGAAACTGATTGTCCAGAAGAGGAGAGCATCCCTCAACGACTTTGACAGGTTCAAGGTTATGTT

upper sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 3
gttggtacaagttttcacggagaaattgttattttattggaagc-atttctttttgttcat---cagtttgttttctcattgaac------agATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
||| |||  | | ||      |   |    ||  |||  | ||  |||| ||| ||| |||    | | ||  |  |  ||   |      ||||||||||||||  |||||||| || || |||||||  || || ||||| ||||||||||| || || || ||||||||||| ||||||||| | |||||
gttagtatgaatgtt------gtgctaccaatcctatcagcagttatttatttctgtccatgtctaatctgagtggtggttattctatttaagATGTTAAGAACAAGTGGGAGAATAGCTCATGGGGCAAGAAGCTAATTGTCCAGAAGAGGAGAGCGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTT

upper sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------gttggtacaagttttcacggagaaattgttattt-tattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
                                             ||  | ||| || |       | ||  ||     ||   |||   |  |  ||  || |||  ||  | ||||  ||   ||||||| |||| ||  |||||||| || || |||||||  || |||||||| ||||||||||| ||||| || ||||||||||||||||||||  | ||| |
gtaactctagagcttatgttgtggacctctttagcaccgccacactttattcaacttctatattctagatgattgcccataagagaatggtgacacttatttgatctcttgctattctttttt--cagATGTGAAGACCAAGTGGGAGAACAGCTCATGGGGCAAGAAGCTGATTGTCCAGAAGAGGAGAGCATCGCTCAATGACTTTGATAGGTTCAAAGTCATGCT

upper sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028883_T01 (Zea mays), 3'ss of exon 3
gttggtacaagttttcacggagaaattgttattttattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
  || |  |  | | |  |||   ||| || |  || |      || ||| |  |  || |   |  | | || | ||  ||||||| || | ||  |||||||| || || |||||||  || |||||||| ||||||||||| ||||| || ||||||||||| ||||||||| | |||||
-gtgatttac-tgtccctggactcattctt-taatacttacctgatgtctata-gcccacctcatcctatcctgactg--cagATGTGAAAAGCAAGTGGGAGAATAGCTCATGGGGCAAGAAGCTGATTGTTCAGAAGAGGAGAGCATCACTCAATGACTTTGACAGGTTCAAGGTCATGTT

upper sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G27090.1 (Arabidopsis thaliana), 3'ss of exon 3
gttggtacaagttttcacggagaaattgttattttattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
||  || |      | | | | | |||   |||||    ||||  ||||  | |  | |   |     | |         ||||||| |||||||  |||||||| || || ||||| || || || || ||||||||  | |||||   |||||| |||||||||||||||||||| |||||
gtgagtgctg--cgtaatgtaaatatttgaatttt----gaagtgtttcaatct--taactggaaaagtctt-------gcagATGTGAAGAACAAGTGGGAGAAAAGCTCATGGGGTAGGAAGCTTATCGTGCAGAAACGTAGGGCTAACCTTAACGACTTTGATAGGTTCAAGATCATGTT

upper sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G20450.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gttggtacaagttttcacggagaaattgtta-ttttattggaagcatttctttttgttcatcagtttg-----ttttctcattgaa--------cagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
      ||| |  |   |      ||  | | ||   |||||||||   | ||| || |||||  |  | |||     | ||  |  | ||        ||||||| |||||||  |||||||||||||| ||||| || ||||| |||||||||||||| || ||  |||| ||||| ||||| ||||||||||| |||||
gtgagtttgttgtagcatacttttgattattcgtaggttttattgg--cctttttttgttgttggttgggttgggtcatcttagctctaaagttatatgcagATGTGAAGAACAAGTGGGAGAAGAGTTCATGGGGTAGGAAACTTATTGTGCAGAAGAGAAGAGCTGCCCTCAATGATTTTGACAGGTTCAAGATCATGTT

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|151408686|gb|EV278494.1|EV278494
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|31474545|gb|CD416573.1|CD416573
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|7639446|gb|AW733769.1|AW733769
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|41146190|gb|CK606401.1|CK606401
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|192299057|gb|FG990385.1|FG990385
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|31309420|gb|CD394623.1|CD394623
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|151405848|gb|EV275663.1|EV275663
EST:     TAAGAGGATCCCCAAGAAGAAGGTTCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|192326906|gb|FK019198.1|FK019198
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|192310170|gb|FK000678.1|FK000678
EST:     TAAGAGGATTCCCAAGAAGAAGGATTTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|58023951|gb|CX710692.1|CX710692
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|209701605|gb|BW655866.1|BW655866
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|31461690|gb|CD403718.1|CD403718
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATGGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|298169651|gb|HO021011.1|HO021011
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|254348775|gb|GR852454.1|GR852454
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|192310169|gb|FK000677.1|FK000677
EST:     TAAGAGGATTCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|209701606|gb|BW655867.1|BW655867
EST:     TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
genomic: TAAGAGGATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGC
EST: gi|298171857|gb|HO021449.1|HO021449
EST:     GATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTG                         ATGTTAAGAACAGATGGGAGAAGAGTTCTTGGTGGCAGAAAACTGATTGTG
genomic: GATCCCCAAGAAGAAGGATCTCATTCAAGCCATGGAGGCTGCTGgttggtacaa ... cattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGG-GGCAGAAAACTGATTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT
                                   tttgttttctcatt  CT-rich tract
                atttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtacaagttttcacggagaaattgttattttattggaagcatttctttttgttcatcagtttgttttctcattgaacagATGTTAAGAACAGATGGGAGAAGAGTTCTTGGGGCAGAAAACTGATTGTGCAGAAGAGGAGGGCATCCCTTAATGACTTTGATAGGTTCAAGATAATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG