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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttatccaatttgtcactgaatattgtcaacatatgcagaaaatatttgtagaaaatgcagtaaattgtgtattttgactttgatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG

Basic information

species Glycine max
transcript GLYMA10G30900.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 3
---ggcttatccaatttgtcactgaatatt--gtcaacatatgcagaaaatatttgtagaaaatgcagtaaattgtgtattttg--acttt--gatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
    |  | || ||| |||  ||| | |||  ||       |       |  | |||  | | |   ||  | |||  |  |||  |||||   |   | |  ||||||| ||||||||||| ||||| ||||| ||| | || |||||||| |||| |||||||||||||  ||| || ||||| | ||| |||
gtttgtatctctaatatgtt-ctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 3
---ggcttatccaatttgtcactgaatattgtcaacatatgcagaaaatatttgtagaaaatgcagtaaattgtgtattttg--acttt--gatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
    |  | || ||| ||   ||| | |||     ||  ||| |  | | | |||  |   | ||||  | |||     |||  |||||  ||     |  ||||||| ||||||||||| || || ||||| ||| | || |||||||| |||| |||||||||||||  ||| || ||| | | ||| |||
gtttgtatctctaatatgct-ctgcagatt-----cagttgctgccact-tatgtgcatgtttcagttgactgttccccttgttacttttggacaaacttctttcagGAAAGTATGTTGGGAATCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGCAAAGACAAAAG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------ggcttatcc-aatttgtcactgaa----tattgtcaacatatgcagaaaatatttgtagaaaatgcagtaa-attgtgtattttgactttgatgtcttgatttca------------gGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
                                    |  | |||   || | |||    |    | ||||||  |  ||    |    | |||   | |  || |    |||   ||| ||| |||| |    ||||||||            ||||||||||||||||| ||||| ||||||||||| |||||||  ||||  ||||| |||||| | || ||    || | ||| |||
gtaagcaccttgtttttagtttctgtttgatgtgttgcttcatcttgatatctcatctcactgtttttgtcagaacttgttatatgattctgttctataatcactgtcgttgaacattctga-tttggtccactgatttcatatgaatacacagGTAAGTATGTTGGAAATCGTCCGATAAAACTACGAAAGAGTAGCTGGAAAGAGAGAACAGATCAGGAGGCTGCTGAAAGACAAAAG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 4
------ggcttatccaatttgtcactgaatattgtcaacatatgcagaaaatatttgtagaaaatgcagtaaattgtgtattttgactttgatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
       | |    || | |       | ||  ||      ||  ||||||  ||||      ||  | |   ||   ||| |||| ||  || ||    ||||||| ||||||||||||||  | || || |||||||| ||||| || |||| |||||||||||||| ||||||  |||| | ||| |||
aggttatggtggctcattataatgactagtaaagtttgagcattgagaaaagttttg-----gatataatggcttaaatatgttgatttaaatctca-attttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 4
----ggcttatccaatttgtcactgaatattgtcaacat--atgcagaaaatatttgtagaaaatgcagtaaattgtgtattttgactttgatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
     ||| |      |  | ||| || ||    |   |  |||  || ||  ||| |      |  | | | ||  |||| |||| ||  || ||    ||||||| || |||||||||||  | || || |||||||| ||||| || ||||||||||||||||||| ||||||  |||| | ||| |||
acgatgctgaaggttataatgacttaaaataacaagttttaatgttgagaa-gtttctg----ctataatgacttacgtatgttgatttaaatctca-attttcagGAAAATATGTTGGAAATAGGCCAATCAAACTACGTAAGAGCAATTGGAGGGAGAGGACAGATTTTGAAGCCTTGGAAAGACAAAAG

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|22523081|gb|BU081892.1|BU081892
EST:     GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
EST: gi|208150188|gb|GD950247.1|GD950247
EST:     GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
EST: gi|254348659|gb|GR852338.1|GR852338
EST:     AGCTTTGCCAATCCTTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAA
genomic: AGCTTTGCCAATCCTT-CTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAA
EST: gi|15664653|gb|BI702024.1|BI702024
EST:     GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
EST: gi|193355864|gb|FK323473.1|FK323473
EST:     GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
EST: gi|207809104|gb|GD781738.1|GD781738
EST:     GCTTTGCCAATCCTTCTGACCTTGCTGGTNCTACTTAAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACT
genomic: GCTTTGCCAATCCTTCTGACCTTGCTGGTGCT-CTTAAA-GAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACT
EST: gi|6341837|gb|AW164661.1|AW164661
EST:     GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: GAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
EST: gi|207793984|gb|GD763874.1|GD763874
EST:     CCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG                         GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG
genomic: CCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagt ... ttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtagaaaatgcagtaaattgtgtattttgactttgatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG
                  taaattgtgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttatccaatttgtcactgaatattgtcaacatatgcagaaaatatttgtagaaaatgcagtaaattgtgtattttgactttgatgtcttgatttcagGTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA