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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT

Basic information

species Glycine max
transcript GLYMA09G38530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 2
-------attttgtaggctattgcatgtagcttctattattgtgt-tatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
       | ||  |||  |||||  || || ||  |   || | |  |  |||||| || ||| |   ||| || | | | |||| | ||    ||   |  |  ||| |||  ||||||||||||||||||||||||||||||||| ||  ||||||||||| ||||||| |||||| | |||||||||||| ||||||||||||| 
ttgtgtcaattcatag--tattgtgtgaagttttcagctttctttgcaactatcatata-gta-aggctatcttaatgattttttttgtt----atgctatactgcagAGGCCAGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGCTGGA

upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G012416_T04 (Zea mays), 3'ss of exon 2
---at-tttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
   || ||| ||   |||||  |  | ||| | |       ||   |  ||    || ||  || ||||  |  |   ||| ||||  | |  |       ||| ||||||||||||||||||||||| ||||||||||| || ||  ||||||||||| ||||||| |||||| | || ||||| ||||||||||||| ||| 
tttatgtttatactgtattg-gtagaacttatttggagagtttgcatggcagtattgcatg-ttcatgt--aatccactttattttcctcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAATATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTTCAGATCTATTTGGATAATGGTGGA

upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
-attttgtaggctattgcatg-tagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccc-----cagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
 || || ||  ||||   ||| ||     ||||  ||     |||  ||||   ||||  |  ||||| |||   ||  | || ||||    ||||        ||| ||||||||||||||||||||||| ||||| ||||| || ||  ||||||||||| ||||||| |||||| | |||||||||||| ||||||||| ||| 
catgtt-tatactatataatggtaaaacttatt--tgcagagtttg-catggcagtat--tgcatgttcaggtaattcacctt-gttttctgcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA

upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
 ||    |  |   | | | | |  | | |  | |    | || | ||||   ||  |||| | |  |  ||       | |  |||| |  |    ||| || ||||||||||||||||||||||||||||||||||| || |||||||||||||| || || ||||||||||||||||||||    ||||||||||||
gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgt--acgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT

upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
--attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
   || | || | | || ||| |    |     |||||     | | ||| || || ||   |   |||    | |    || ||||||| |  ||    || || ||||||||||||||||||||| ||||||||||||| || || |||||||| || || || |||||| | || ||||||||| ||||||||||||||
ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcat-taagtttagaatg-attgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT

upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 3
attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtat-gtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
   | | | |  | | || |||||    ||| |||   | | | |    |||   ||   ||    | || || || || ||||||| | |   |  |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||| ||||  | ||||||||||||||||||||| ||||||||||||||
tggtggaaagtaactaca-gtagcgaacattcttgacgtgtgtttttgttatcaaatttgttgacataagcctgttgtcatttgtttctatttttttccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAGCGCCGCTGGACCCTGCAACATTTGCAGATGCAGTGGTCCAGATTTATCTGGATAATGCTGGT

upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ06557 (Selaginella moellendorffii), 3'ss of exon 2
attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctca-atccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
                                 |  |   |||   ||   || ||   || || |  || |   ||  ||  |   |      |    ||||||||||||||||||||||||||||||||||||||    ||| |||||||  |  | ||| |||||||  | |||||||| || |||||| ||||||||
--------------------------------gtaagggctttgagattcttgcattggttttggtttggtttggtttgttcatgatttgggcgtgtatagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAATTCCGTTGGACCCATCTTCTTTCGCGGATGCTATAGTCCAGATCTACTTGGATCATGCTGGT

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|26045706|gb|CA783207.1|CA783207
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|5687979|gb|AI940994.1|AI940994
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|209717990|gb|BW671821.1|BW671821
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|5057528|gb|AI736004.1|AI736004
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|7284994|gb|AW597481.1|AW597481
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|21286052|gb|BQ473923.1|BQ473923
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCACCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|16104801|gb|BI892541.1|BI892541
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCACCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|10709482|gb|BF009206.1|BF009206
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|13480362|gb|BG509705.1|BG509705
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|20449584|gb|BQ253708.1|BQ253708
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|120533835|gb|EH261968.1|EH261968
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|6726947|gb|AW311227.1|AW311227
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|7042245|gb|AW472139.1|AW472139
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|120533411|gb|EH261544.1|EH261544
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|16347133|gb|BI972728.1|BI972728
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|6724745|gb|AW309144.1|AW309144
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|16997181|gb|BM086553.1|BM086553
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
EST: gi|120533741|gb|EH261874.1|EH261874
EST:     GCTCGAAGGAGAGACCCACTCTTGG                         TGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC
genomic: GCTCGAAGGAGAGACCCACTCTTGGgtacgattcg ... caatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
                         ctcttttcttttgttt  CT-rich tract
     atgtataatttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - -gcatgta
- - - - - - - - - - - gcttcta
- - - - - - - - - - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgagg