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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatccacatctcactgtgtcaactttgtttttattattgtgtatcgtgtactacacacagcacaatcaatttagtctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT

Basic information

species Glycine max
transcript GLYMA03G32800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 2
gatccacatctcactgtgtcaactttgtttttattattgtgtatcgtgta-ctacacacagcacaatcaatttagtctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
  | || || |     | | |         |    |||   |||  | || ||| |       |    || ||  |  |   |      |  |  || ||||| || || || || ||||||||||| ||||||||||||||||| ||||| || || ||||| ||| | || ||||| || ||||||||||| ||| | |
-gttcatatttttgcatatgattaaaaaggtgcaaatttgatattatatagctatattttttccttgaaaattcatgaatatctttttgtaattattgcagGCGGTTGCTAATTCTACATCAGCAACATTTTTGCGTGTTGTTGGGAGTGAGTTGATCCAAAAGTACCTTGGTGATGGCCCCAAGCTTGTAAGAGAATTGT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------gatccacatctcactgtgtcaactttg--tttttattattgtgtatcg---tgtacta-----cacacagcacaatcaatttagtctaatacaaacccttt------tactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                                                 || ||    |||      ||  | ||  || | || |||  | |  |   || ||||     ||  | | ||     | ||     |  ||  |    ||      |  || |||||||| || ||||| ||||| ||||| || |||||||||||||| |||||  | || ||||| ||  | || |||||||| || || || |||||||| |
gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------gatccacatctcactgtgtcaac-tttgtttttattattgtgtatcgtgtactacacacagcacaatca--atttagtctaatacaaacccttt-----tactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                                                                 |  | ||||  || |||| |  ||| |    ||||   | | |  | ||||   ||     |||  |  || || |    ||   |    ||     |   | ||||||||||| ||||||||||| || || || ||||||||||||||||||||| | || ||||| ||| | || |||||||| || || ||  | ||| | |
gtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcaggctttgatatctgcctttgtctatgtttatccaaattacactctttt-tctacttttcagttttcaaatagcatgtacttgggtagtgattacttgaaactgtctgcagGCTGTGGCTAACTCAACATCTGCGACTTTCTTGCGTGTTGTTGGTAGTGAACTCATTCAAAAGTACCTTGGGGATGGTCCCAAACTAGTCCGAGAATTGT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------gatccacat-ctcactgtgtcaactttgtttttattattgtgtatcgtgta---ctacacacagcacaatca-atttagtctaatacaaacccttttacttt-cagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                                                                                  || |   |  ||     |      ||| ||  |   ||    |||  | ||   ||  |  |   | ||||| ||||    || |  ||||  ||  ||  |  ||||||| || || || || |||||||| || |||||||||||||| |||||||| || ||||| ||| | || |||||||| |||||||| || ||| | |
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcc-taaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------gatccacatctcactgtgtcaactttgttt-----ttattattgtgtatcgtgta--ctacacacagcaca-atcaatttagt--ctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                                                                                 ||   | | |  || |||  |  |   ||     ||||| || | ||   |  |   | || | ||||   |       |||  ||| |  ||||  |||    | |||||||| || || |||||||| || || || ||||||||||| ||||||||| | || ||||| ||| | || |||||||| ||||| || || ||| | |
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttc---tgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 2
gatccacatctcactgtgtcaactttgtttttattat-tgtgtatcgtgtactacacacagcacaatca-atttagtctaatacaaaccctt-tta--ctttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
     |    |   ||         | |||||| | | | | |   |  |  || |  | | ||  |   |  |   | | |   |   ||| |||  ||||||||| |||||||| || || ||||| || || ||||||||||| ||||||||| | || || || || || ||||||||||| |||||||| ||||||||||
-----atggattgttgcagtgtgcctctttttaatgtgtctcttatgcttgttaaattcggaactgttggagatgagcaagtgttatttcttgttattctttcagGCAGTGGCAAATTCTACTTCAGCTACTTTCTTGCGTGTTGTCGGTAGTGAACTGATTCAGAAGTATTTAGGAGATGGTCCCAAGCTTGTGAGGGAACTTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
gatccacatctcactgtgtcaactttgttt-ttattattgtgtatcgtgtactacaca-cagcacaatcaatttagtctaa----tacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
        |||  || | ||   | | | | | |  |   ||       | | |       |    ||| | |  |  |||    |  ||     | |  ||| |||| || || || ||||||||||| || || ||| | ||||||||||||||  | || || || || |||||||||||||| |||||||| || |||||||
------tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 2
gatccacatctcactgtgtcaactttgtttttattattgtgtatc-gtgtactacacacagcacaatcaatttagtctaatacaaacccttt-tactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
  |       | ||| |    |  || || || |  |||   ||| | |||     |    || | |   | ||  ||   |     | ||| |    |||||| || |||||||| ||||||||||| || || ||||||||||| ||||| ||||| |||||||| ||||||||||| |||||  | || |||||  | |
-ctttgttatttacttttcttatattcttgtt-tagttgaagatcagagtagcttccttgtcaaagttgttctaaacttgcaaccctcatttatgtactcagGCAGTTGCAAACTCTACATCAGCAACTTTCTTACGTGTTGTTGGCAGTGAGTTAATTCAAAAATATTTGGGAGATGGGCCAAAATTAGTGAGGGAGTTAT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 2
gatccacatctcactgtgtcaactttgtttttattattgtgtatcgtgtactacacacagcacaat-caatttagtctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                                               ||   |||      |   | |   || ||  | ||   | | ||     | |||||||| |||||||| ||||| ||||| || |||||||||||||| || ||  | || ||||| || |||||||| ||||| |||||||| ||||| || |
-------------------------------------------gtaagtgtgacatcttttaaggtgctgcttcgta-actaactagctttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 2
gatccacatctcactgtgtcaactttgtttttattattgtgtatcgtgtactacacacagcacaatcaatttagtctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                                        |||   |||   |  |   | |    | | || ||  | ||   | | ||     | |||||||| |||||||| ||||| ||||| || |||||||||||||| || ||  | || ||||| || |||||||| ||||| |||||||| ||||| || |
----------------------------------------gtaa-atgtgacat-ctttgaaggtgctacttcgta-attaactagctttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

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|13789045|gb|BG651636.1|BG651636
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|6725713|gb|AW310112.1|AW310112
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|58019738|gb|CX706480.1|CX706480
EST:     AGTTATTTTATATGGGGAACCAGGAACTGGGAAGACA-TGCTTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGA
genomic: AGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGC-TTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGA
EST: gi|207825455|gb|GD800554.1|GD800554
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|16996954|gb|BM086326.1|BM086326
EST:     GAGTTA-TTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|151412684|gb|EV282496.1|EV282496
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtactacacacagcacaatcaatttagtctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
                            gtctaat  putative branch site (score: 3)
                                        cccttttactttc  putative PPT
                      aatttagtctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatccacatctcactgtgtcaactttgtttttattattgtgtatcgtgtactacacacagcacaatcaatttagtctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- -ccacatc
- - - - - - -ctgtgtc
- - - - - - - - - - - - - - - - - - - - - - cgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - acacaca