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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaagtatgtctgaagttcaataaaatcagtgttgatattctgtatttatttatctcgtgaatggtactgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG

Basic information

species Glycine max
transcript GLYMA11G34130.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g16570.3 (Oryza sativa), 3'ss of exon 8
acaagtatgtctgaagttcaat---aaaatcagtgttgatattctgtatttatttatctcgtgaa-tggtactg-acaccttgtttatgtttttattt--tttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG
       | | |    ||| ||   |  ||     ||| |  | | || || ||| | || |||  ||| |||| |    ||  |||  ||   | ||  |||| ||||||| || |||||||||||||| ||| |||||||||| || |||||||| || || ||    || |   |   ||| |||  ||   | | | ||  | 
------gtttttagctttccatcgaaggattgacattggtgctat-tagttttttgtgtcatgaggtgggactgcaaggtttacttactttcccacttgttttgcagTTTCATGCAAACTGCATCGATCCATGGTTGCGCCAACAGGGAACATGCCCAGTTTGCAAGCACCGTGTAAGCGATGGGTGGCATGGTGAAGCAGATGCTT

upper sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G492252_T02 (Zea mays), 3'ss of exon 7
acaagtatgtctgaagt-tcaataaaatcagtgttgatattctgtatttatttatctcgtgaatggta---ctgacaccttgtttatgtt--tttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG
      | | | ||  | |  | ||||  |||||| || |  ||| |     |    |   ||| | |   |||  |  ||  |||  ||   || | ||||| |||||||||  ||||||||||| || |||||||||||||| || ||||||||  | || ||    |  |   |   ||| |||  || ||  ||  |   ||
------aaggcagagctcttcaaaaaagaagtgttaatgtgatgtgtcctgatgaggcaacaatcgcaacactgcaagatttcttactttgtcttttgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTCAGTGATGGGTGGCATGCCACAGGCAACGGTG

upper sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
acaagtatgtctgaagttcaataaaatcagtgttgatattctgtatttatttatctcgtgaatggta---ctgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG
  | | | | | || | ||  |||||  |||  | || |  |||       |    |     ||| |   |||  |  ||  ||||  | || | ||||  |||||||||  ||||||||||| || |||||||||||||| || ||||||||  | || ||    |  |   |   ||| |||  ||  |  ||  |   ||
--atgcaaggcaga-gctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG

upper sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g05080.t01 (Vitis vinifera), 3'ss of exon 7
--acaagtatgtctgaagttcaa-taaaatcagtgttgatattctgtat-ttatttatctcgtgaatggtactgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG
   ||  ||  | |    |  || | || |   | |||||||   ||||   ||| |  | ||      |  |||||  ||||   || | ||||  |||  |||| || || ||||| || ||||| |||||||| |||||||| ||||||||||| ||||||||| | |  ||  | || |||   || |   |  | | ||
ttgcatctaactttaggttggaaatgaagtttatcttgatat---gtatgccattcaatttgttttatattttgacat-ttgtaactgctattatgattttcagTTCCATGCCAACTGTATTGATCCATGGCTGCGACAACAAGGCACATGCCCTGTCTGTAAATTTAGGGTCGGGGCAGGATGGCAGGAGAGCAGGGAGAGTG

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|214008417|gb|DB989983.1|DB989983
EST:     AGCAAGTTGATGTTGGTGACGTACTGCGTAGCTTACCTTGCTTGCATCAG                         TTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCT
genomic: AGCAAGTTGATGTTGGTGACGTACTGCGTAGCTTACCTTGCTTGCATCAGgtttatttca ... ttttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCT
EST: gi|209705961|gb|BW661778.1|BW661778
EST:     AGCAAGTTGATGTTGGTGACGTACTGCGTAGCTTACCTTGCTTGCATCAG                         TTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCT
genomic: AGCAAGTTGATGTTGGTGACGTACTGCGTAGCTTACCTTGCTTGCATCAGgtttatttca ... ttttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCT
EST: gi|298179910|gb|HO025125.1|HO025125
EST:     AGCAAGTTGATGTTGGTGACGTACTGCGTAGCTTACCTTGCTTGCATCAG                         TTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCT
genomic: AGCAAGTTGATGTTGGTGACGTACTGCGTAGCTTACCTTGCTTGCATCAGgtttatttca ... ttttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttatctcgtgaatggtactgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG
                    tactgac  putative branch site (score: 1)
                                     tgtttttatttttt  putative PPT
                              ttgtttatgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaagtatgtctgaagttcaataaaatcagtgttgatattctgtatttatttatctcgtgaatggtactgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG