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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG

Basic information

species Glycine max
transcript GLYMA05G03150.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 2
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
   ||      ||  |   |    ||  ||| |   |||  | | |     |   ||| ||   |||   |||     || || | ||  ||  ||||||     ||      || ||||| ||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| ||||| |
caaagaaaaatcttgtatgtgtgcttaagtt-caaaatctcgtaaagaaaaaatgtatgta---cacccgtttgc---ttattctggttttgtgtgatttactttagAAATCGGACTTGGAGAAGGCGCAGCTTGGCCTGGGTCATAGCTACAGCAGGGCGAAGGTGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGG

upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
  |  ||       |||| |   |   |   | |||  |  | | |      | || ||  | | | |  ||  |   ||| |  | || |  | ||||     ||| |    || ||||||||||| || || || ||||| ||||| || |||||||||||||| ||||| ||||| |||||||| || |||||||| |||||||
--tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgtt-ttcgatt----gcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG

upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 2
gttagtgtttcctcatgcctccttttgtgtttctgtatc-caggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
  |  ||      |      | |||| | |  ||  ||    | | | ||  |       | |     ||||||   | |    | ||| |   |||||| |    ||  |   || ||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || ||||| || |||||||| || ||||
--tgatgagcttacgcattgctttttatatgcctaaattgttgtaaagctaaacgcctgctgtgct--taatttggctttaccatgtgtccatgttgattgt----agGATTCTGACTTGGAGAAGGCCCAACTTGGCCTGGGGCATAGCTACAGCAGGGCTAAGGTGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAG

upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 2
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttg-atttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
        | |   ||     ||  || | || || ||   | |      | | || |  |  |   |  || || |  |   |||||  | |      |  |   ||  |   || ||||| ||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || ||||| ||||||||||| || || |
--------tgcaaaattttggctgctgggcttatgcatagtgtatcaaattttgttgtgaagttggatgcttgatgtgcttaatttgtttttccgatggtgattgtagGATTCTGACTTGGAGAAGGCCCAGCTTGGCCTGGGGCATAGCTACAGCAGGGCCAAGGTGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGG

upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctg--cttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
                |  |  | |  | | | ||| |  |  |    | | |||  |||   |  || || |   |  |||| |  |       ||   |||    || |||| ||| | |||||  | || |||||  | |  || || |||||||| || ||||||||||| ||||||||||| || || ||||||||||||||||
----------------gtgtgatctcctttctatgtgtttaaaatctttttgtct-gtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG

upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
                         ||||||| |   |   |   ||||    | ||   ||||   |  | |   |  |   | |   || ||| ||  |    || |||| ||||||||||| || |||||||| || |  ||||| |||||||| |||||||||||||| ||||||||||| || || ||||||||||||||||
------------------------gtgtgttttttatttttgattacctaatacctacacatatttttgctattcgtgctcaatatcatcttctttataat--gtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG

upper sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
----------gttagtgtttcctc--atgcctccttttgtgtttctgtat-ccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttc--acagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
           ||| | |||||    |    | ||| ||  ||| ||| |   |  |||  |  |   ||      |   |  |||  | |||  | || |  |  ||  |||| |    || |||||||  | |||||||| ||||||||||||||||| ||||||||||| |||||||||||||| ||||| ||| | || || || ||||| ||||| |
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcg-gtattttctttgca-atttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG

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|298197837|gb|HO039376.1|HO039376
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCA
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCA
EST: gi|298197821|gb|HO039360.1|HO039360
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|208288849|gb|GE086654.1|GE086654
EST:     CTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGTATTCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAG
genomic: CTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTG-A-TCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAG
EST: gi|193357442|gb|FK321926.1|FK321926
EST:     CTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: CTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|208279963|gb|GE076311.1|GE076311
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|254320642|gb|GR827091.1|GR827091
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|207746786|gb|GD721087.1|GD721087
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGTACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|254314031|gb|GR831660.1|GR831660
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|209710464|gb|BW662000.1|BW662000
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|209719024|gb|BW674838.1|BW674838
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAACAGGCACAACTTGGTCTGGGACATAGT
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGT
EST: gi|298193904|gb|HO040552.1|HO040552
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|254322077|gb|GR837491.1|GR837491
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|15812968|gb|BI785243.1|BI785243
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|16349266|gb|BI974861.1|BI974861
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
EST: gi|213620394|gb|DB957291.1|DB957291
EST:     TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAG                         TCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG
genomic: TTCTTCGTGGTGTGCGATTCCATTTTGATACGTTTGTTGGTGATCTCAAGgttagtgttt ... tttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
                                             tttttcac  CT-rich tract
     tttatatcactaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG