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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaataatttataacttcattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT

Basic information

species Glycine max
transcript GLYMA20G33630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G04850.2 (Arabidopsis thaliana), 3'ss of exon 2
gaaataatttataacttcattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT
                   |   | |||  | |     |   |    |||| | |||    |  || |||   ||| |||     |     |||  ||||||||||||| || ||||||||||| || |||||||| || || || |||||||||  |||||||||||| ||| ||||||||||||||||||||
------------------gtcagtgttttctttctgcttcttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT

upper sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 3'ss of exon 2
--gaaataatttataacttcattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttgg----ttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT
   |   | |  | |   | ||| | |||         ||   |  |    ||  ||||  ||     |  | ||| | ||    | ||    |||      ||||||||||||| || || |||||||| || |||||||| ||||||||||||||||||  ||| || ||||| ||  | ||||||||||||||||||
gtcagtcactagacattgttatttaaattgatccagcaagctaagctactctgtttattggatttgcttgataataaaacacctaagtacatttttatgaatttagGTATGAAGGACAACGCGACATGCTCTATAATCAGACATTCAATCTCGATCAAGTTTCATTCGCCGCTGAAGGACTCAAAGATGCTCAACAAACT

upper sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
-gaaataatttataactt-cattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT
  |||  || ||     | | | ||   | | |  ||   | |   |   || ||| |||| |  |   |||  ||  |  |  |  ||||| |||| | ||||||||||| |||||||||||||| ||||| || || ||||| || || ||||||  |||||| ||||| || |||||||||||||| ||||||
taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaattttatgttccacaatt--taaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT

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|298174856|gb|HO014773.1|HO014773
EST:     CAGGAGGCTGTTAAAGCTAGAGCTATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|254325618|gb|GR838499.1|GR838499
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|298171425|gb|HO016457.1|HO016457
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|298163684|gb|HO012417.1|HO012417
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|192326636|gb|FK018853.1|FK018853
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|254338846|gb|GR847563.1|GR847563
EST:     CAGGAAGCTGTTAAAGCTAGAGCCCTGAGAGTTCTTAACCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATC
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATC
EST: gi|208048063|gb|GD849206.1|GD849206
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAA
EST: gi|151397618|gb|EV267491.1|EV267491
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|298199136|gb|HO042499.1|HO042499
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|298176762|gb|HO023235.1|HO023235
EST:     TCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTACAATCTCGATCA
genomic: TCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|192314082|gb|FK010362.1|FK010362
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
EST: gi|192294647|gb|FG986496.1|FG986496
EST:     CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAAT                         GTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA
genomic: CAGGAAGCTGTTAAAGCTAGAGCCATGAGAGTTCTTAAGCAAAAACGAATgtgagtttgc ... ctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT
                                          tgccttt  CT-rich tract
      aatattatatagct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaataatttataacttcattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - -cattcat
- - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcac