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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactacaaacagcacaatcagtttggtctaacacaaaggcttgcttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT

Basic information

species Glycine max
transcript GLYMA19G35510.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 2
gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactaca-aacagcacaatcagtttggtctaacacaaaggcttgcttac-----tttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
        ||||  | |    | || ||  |    ||    |  |  | || | | |   |   |    |||      ||  ||    |  ||       || ||||| || || || || ||||||||||| ||||| ||||||||||| ||||| || || ||||| ||| | || ||||| || || |||||||| ||| | |
------gttcatatttttgcatatgattaaaaaggtgcaaatttgatattatatagctatattttttccttgaaaattcatgaatatctttttgtaattattgcagGCGGTTGCTAATTCTACATCAGCAACATTTTTGCGTGTTGTTGGGAGTGAGTTGATCCAAAAGTACCTTGGTGATGGCCCCAAGCTTGTAAGAGAATTGT

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactacaaacagcacaatcagtttggtctaacacaaaggcttgct-----tactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
                                                                   || || |  | |||| | |  ||| |    ||||   | | |    |  |   |      |||  ||  ||  ||     |  |  |   |     |   | ||||||||||| ||||| ||||| || || || || |||||||||||||||||| | || ||||| ||| | || |||||||| ||||| ||  | ||| | |
gtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcaggctttgatatctgcctttgtct-atgtttatccaaattacactctttttctacttttcagtttt-caaatagcatgtacttgggtagtgattacttgaaactgtctgcagGCTGTGGCTAACTCAACATCTGCGACTTTCTTGCGTGTTGTTGGTAGTGAACTCATTCAAAAGTACCTTGGGGATGGTCCCAAACTAGTCCGAGAATTGT

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 2
--gacatgtctcattgtgtcaactttgtttttat-tattgtgtgtggggaactacaaacagcacaatcagtttggtctaacacaaaggcttgct-tactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
  |   |||  || |||| |   |||   | | | | || ||  ||   || |   ||| |     |     ||  | |     |   |||| | | ||||||||| |||||||| || || ||||| || || || |||||||| ||||||||| | || || || || || ||||||||||| || ||||| ||||||||||
atggattgttgcagtgtgcctctttttaatgtgtctcttatgcttgttaaattcggaactgt----tggagatgagcaagtgttatttcttgttattctttcagGCAGTGGCAAATTCTACTTCAGCTACTTTCTTGCGTGTTGTCGGTAGTGAACTGATTCAGAAGTATTTAGGAGATGGTCCCAAGCTTGTGAGGGAACTTT

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 2
gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactacaaacagcacaatc----agtttggtctaacaca--aaggcttgcttactt--tcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
        |  || | |  |||||  || |||| |||| |    | |  |   |  |||    |     |  ||| |||||      ||  ||   |||  |  |||||| || |||||||| ||||||||||| || |||||||||||||| ||||| ||||| |||||||| ||||||||||| |||||| | || |||||  | |
------ctttgttattt--acttttcttatattcttgtttagttgaagatcagagtagcttccttgtcaaagttgttctaaacttgcaaccctcatttatgtactcagGCAGTTGCAAACTCTACATCAGCAACTTTCTTACGTGTTGTTGGCAGTGAGTTAATTCAAAAATATTTGGGAGATGGGCCAAAATTAGTGAGGGAGTTAT

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 2
gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactacaaacagcacaatcagtttggtctaacacaaaggcttgcttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
                                    ||  ||| |  |      |  |  |      |     |||||    ||  ||| ||   | |||||||| |||||||| ||||| ||||| || || ||||||||||| || ||  | || ||||| || |||||||| ||||| || ||||| ||||| || |
------------------------------------gtaagtgtgacatcttttaaggtgctgct--tcgtaactaac---tagctttggtt--ctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 2
gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactacaaacagcacaatcagtttggtctaacacaaaggcttgcttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
                                    ||   || |  |      |  |  | |    |      ||||    ||  ||| ||   | |||||||| |||||||| ||||| ||||| || || ||||||||||| || ||  | || ||||| || |||||||| ||||| || ||||| ||||| || |
------------------------------------gtaaatgtgacatctttgaaggtgctact--tcgtaattaac---tagctttggtt--ctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

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|254326967|gb|GR836576.1|GR836576
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGT
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGT
EST: gi|22541543|gb|BU091386.1|BU091386
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGCGAAGACGTTGCTAGCTAAA                         GCTGTGGCCA-CTCGACATCA-CAACCTTTT-ACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|16278683|gb|BI943034.1|BI943034
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|208060774|gb|GD856696.1|GD856696
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|192308140|gb|FK000468.1|FK000468
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|254332564|gb|GR846502.1|GR846502
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|209699123|gb|BW656163.1|BW656163
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGNCA-CCTTTTTACGTGTTGTTGGTAGTGA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAG-CAACCTTTTTACGTGTTGTTGGTAGTGA
EST: gi|208330871|gb|GE128532.1|GE128532
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|16276341|gb|BI941808.1|BI941808
EST:     ATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: ATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|298167360|gb|HO012623.1|HO012623
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAGG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|308099190|gb|HO761031.1|HO761031
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|308098232|gb|HO759973.1|HO759973
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|16279118|gb|BI943267.1|BI943267
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|193374174|gb|FK342836.1|FK342836
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTT-ACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|20814952|gb|BQ299430.1|BQ299430
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|27427106|gb|CA938626.1|CA938626
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
EST: gi|16281898|gb|BI944726.1|BI944726
EST:     GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAG                         GCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA
genomic: GAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactacaaacagcacaatcagtttggtctaacacaaaggcttgcttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT
                                          tgcttac  putative branch site (score: 2)
                                            cttactttc  CT-rich tract
                                             ttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacatgtctcattgtgtcaactttgtttttattattgtgtgtggggaactacaaacagcacaatcagtttggtctaacacaaaggcttgcttactttcagGCTGTGGCAAACTCGACATCAGCAACCTTTTTACGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAACTTGTAAGGGAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
-acatgtc
- - - - - - - tgtcaac
- - - - - - - - - - - - - - - - - - - gtgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcttgc