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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA

Basic information

species Glycine max
transcript GLYMA09G28440.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
gtcagtggtacaat--gaatctatgaatttttattttatttt--ttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
|| || | | | ||    | ||||  |||         | |   |    |      || |  |  |  | | |   |     | || ||     |||||| ||||||||||| ||||||||||| || ||||||||| | ||||| || ||| | ||||||||||| ||||||||||| |||||  | || || || |
gtaag-gctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgccctttttt-ttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtg--ttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
       |||       |    |  |   | ||||   |     || |  | || | ||   |   |   | |  |  |       |     |||||| ||||||||||| ||||||||||| || ||||| ||| | ||||| || ||| | |||||||| || ||||||||||| |||||  | || || || |
-------gtatggctcgtacccgtctccgtcttttgcgtggcgcatgggttctgtatgtctcatcatgcgtcgcttgctcacccgcttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttt--tattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
|| | | ||    ||| ||| |  |||||  | ||| | |   | ||| || || | || ||     |||| |    |    || | | | || ||||||| ||||| || ||||||| ||| ||| |||| |||||||| ||| | ||| | || ||||| |||||||| || || |||||||||||||| || |
gtgaattgt---gtgattctgttcattttgttctttcaatggatttatcgtatt-ggaactgttttggtaactgtgttgagattttgattttgtagTTTGTAGCGGACGGTGTGTTCTACGCTGAATTGAATGAGGTTCTTACAAGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCTA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
|| | | ||    | | | | ||  |||| | |  | || |     ||| |     | || |||||  |  ||  || |||      | || ||||||| |||||||| || |||| ||| ||| |||| |||||||| ||| | ||| | || ||||| |||||||| || || |||||||||||||| || |
gtgaattgtgatttcattttttg--ttttcagtggacttctctagctgtatc--gtattggaactg--atctggttactgt-----gtttgtagTTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCAA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 3'ss of exon 1
--------gtcagtggtacaatgaatctatgaatttttattt--tattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
         |  ||  |   ||    || ||  || | |  |   | |       || ||||||  |  |   | |||| ||   | || || |     | ||||| || || |||||||| ||||| || || |||||||||||||| ||  | ||| |||| ||||| || ||||| || || ||||||||||||||||| |
gtctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttct---cttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGAGAGCTGGCCGAGGATGGCTACTCTGGTGTCGAGGTTAGGGTTACGCCAA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttga-aagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
                                                 |||||  |||  |  | |     |      || |  |    | ||||| || || ||||||||||||| |||||| || || ||| |||| || || ||| | |||||||| || ||||| |||||||||||  | || || ||||
-------------------------------------------------gtttgtcaagcaatgccgctccctc--ctctgattctctcttccagTTCGTCGCCGATGGAGTGTTCTACGCCGAGCTCAATGAGCTTCTCACGCGGGAGCTAGCGGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34304 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatg--tgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
                                              | ||||    | ||   ||      |           || ||   | ||||| || || ||||| ||||||| |||||| || |||||| |||| || || ||||| || ||||| || ||||| |||||||||||  | || || ||||
---------------------------------------------gtctgttcagcaatgccgctccctccttctcctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaa-ttgaatagtgttattaatgtgc-agTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
                                              | ||||    | ||   || |    ||      || | | | | | | |||| || || ||||| ||||||| |||||| || |||||| |||| || || ||||| || ||||| || ||||| |||||||||||  | || || ||||
---------------------------------------------gtttgttcagcaatgccgctctccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ31296 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
                                              | ||||    | ||   || |    |            |    | ||||| || || ||||||||||||| |||||| || || ||| |||| || || ||||| |||||||| || ||||| |||||||||||  | || || ||||
---------------------------------------------gtttgttcagcaatgccgctctccccttctcctctgatctctcttccagTTCGTCGCCGATGGAGTGTTCTACGCCGAGCTCAATGAGCTTCTCACGCGGGAGTTAGCGGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

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|23058305|gb|BU578303.1|BU578303
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|5677916|gb|AI939046.1|AI939046
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGCGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|33389542|gb|CA852749.1|CA852749
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|4291003|gb|AI441699.1|AI441699
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|12497107|gb|BG047401.1|BG047401
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|8283729|gb|BE021288.1|BE021288
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|120496311|gb|EH224478.1|EH224478
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|4290831|gb|AI437533.1|AI437533
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGACCTGAACAAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|254325495|gb|GR838376.1|GR838376
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|192305912|gb|FG995462.1|FG995462
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|120496331|gb|EH224498.1|EH224498
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|151406004|gb|EV275819.1|EV275819
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|213592479|gb|DB971635.1|DB971635
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|14990868|gb|BI316541.1|BI316541
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|151409012|gb|EV278820.1|EV278820
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|298179211|gb|HO027682.1|HO027682
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|21889395|gb|BQ742608.1|BQ742608
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|21889541|gb|BQ742754.1|BQ742754
EST:     TCTTCTTCCATTGGCAAACATGGCAACTGCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: TCTTCTTCCATTGGCAAACATGGCAACT-CAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|298164138|gb|HO013783.1|HO013783
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|9564213|gb|BE473722.1|BE473722
EST:     CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAG                         TTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: CTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggta ... taatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA
                                          tattaat  putative branch site (score: 2)
                           taaattgaatagtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG