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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcattggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG

Basic information

species Glycine max
transcript GLYMA18G48370.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggt--tcattggatta---aaattctgctttcatg-attagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
    || |  |   | |  ||   |   |  ||| || |||| | || |  |  | |   |   |    |  |   |||    | |||  | | || |   | || | ||||| ||||||||||| ||||| ||  | |||||||||||||| ||||| ||||||||  | ||||| || ||||| ||||| || ||||||||| 
-agttttttgaacaccatgtt---accgtcccttcctcaaat-atctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG-

upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
-----tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcattggattaaaattctgcttt-catgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
     | ||   |  ||  ||||||| | |  |  | ||  ||   |  | ||| |   | ||     | ||| | | |          || |||   |  | || | ||||| ||||||||||| || || || || |||||||||||||| ||||||||||||||  | ||||| ||||| || ||||| || ||||||||| 
tttcgtcacaatttcagaactagcttatgatga--atttattg---ttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG-

upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcattggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
       | |  | ||   ||| |||| ||||||| |    |    |      | |    |||   |   ||| |    ||   | | |||     ||||||||||| || |||||||| |||||||| ||||| ||  ||||||| ||||||||||| ||||| || || ||||| || ||||| || ||||||||| 
------gtatgatcct---tttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG-

upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G16340.3 (Arabidopsis thaliana), 3'ss of exon 10
-tgacttctgtagttctagcttttaaaaataactttctgaaatgacct---ttccaaatcttacacctggttcat-tggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
 |    ||  |||  | |   | | |   ||| ||    |||||       ||  ||| || |  |    ||  | |  | | |||     |||   |   ||||| ||||| || |||||||||||||| || ||||| ||| ||||||| ||||| ||||| || || || || ||||| || ||||| || ||||||||| 
gtatggtcattagaacgatgctctga--gtaatttaagaaaatgcttggtgttttaaagctaaatcagaattggtctaaactcaaacataccttgtttatatagTTAGATGGTGGGGGTGTTGCTAGTGGTGGCCTTCGCGAATTAATACCATGCATAGCAAGAACCGCCGTAGCTGTTGGTGTCGATGGAATTTTCATGGAG-

upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
-tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcatt--ggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
   | ||   |    |    | ||  | ||  ||     |  |   |||  ||||    | ||   | | ||   |   ||||  |||  |||    |  || |||| || ||||||||||| |||||||||||||| ||| | ||||| |||||||| |||||||||||||| |||||||||||||| || ||||||||| 
taaatttgaatgccacataatattttagatg-ctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctattttt-caaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG-

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|14009134|gb|BG725738.1|BG725738
EST:     TAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGATGT                         TGGATGGGGGAGGTGTTGCAAGTGGAGGTCTTCGAGAACTAATACCTTGCA
genomic: TAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGATGGtgtgtttagc ... catgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCA
EST: gi|192294788|gb|FG987477.1|FG987477
EST:     TAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGATGT                         TGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCA
genomic: TAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGATGGtgtgtttagc ... catgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCA
EST: gi|193699456|gb|FK640289.1|FK640289
EST:     ACAGCCTGCTGGAAAGATGT                         TGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCA
genomic: ACAGCCTGCTGGAAAGATGGtgtgtttagc ... catgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttccaaatcttacacctggttcattggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
        atcttac  putative branch site (score: 3)
                                    ttctgctttc  putative PPT
                        attggattaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcattggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- acttctg
- - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - -ctttctg
- - - - - - - - - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacctg