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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttagatcacaatagtttgaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA

Basic information

species Glycine max
transcript GLYMA14G01290.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 1
tttttagatcacaatagttt-gaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
  |  ||| |     | |   ||   ||     ||| || | | ||| |  ||  |||   || |  |  |  || |   ||||||||  |||   |  ||||||| ||||| || || ||||||||||||||||||||  |||| ||||| || || ||||||||||| ||||| || || ||  | || ||||| || |
agtacagaacttggaactcaagagcatttcatctgttatctatatatagtctgatgatgatttgtattattatttttacatccaatttttaat-cctgcagAGTGTTCTTGGGATCATCCTTGGAGGTGGTGCTGGGACAAGGCTGTATCCGCTGACAAAGAAGAGGGCGAAGCCGGCGGTGCCGTTGGGTGCTAATTACA

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
tttttagat--cacaatagt-----ttgaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
  || | ||  ||||||| |     || |     ||| |||    | |  |  |   ||| |  |  || |   |||    ||||| |   | |    |   |  ||||||||||||| || || |||||||||||||| |||||| |  | ||||| |||||||||||| | || ||||| || || ||||| || || ||||| |
--ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattat--ctcta---ctgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 1
tttttagatcacaatagtttgaattttgatcttgtgatatttgtattggatgt---ggattggttctggttctgattctgattccaatttaaaatgtt-tatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
   | | |||      ||   | |   | |||  ||        | |||||||   ||   | || |    |   |  |   |    |  |     |  || ||||||| ||||| || || |||||||| |||||||||||  |||| |||||||| || ||||||||||| || ||||| || ||  | || || ||||| |
--ataaaatct--gcggtgccagtgccggtctactgggtcagtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 1
-----------tttttagatcacaatagtttgaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
            ||  | | |    |   ||  |||  | | ||||||| ||| || ||| | ||| |  ||| |||||     |||  |              | |  ||||||| ||||| ||||| || |||||||| || || || ||||| || || || |||||||||||||| ||||| || ||||| || || || || ||||
gtcagtctcaccttccaaaccctcttgtgttttattggggttttgtgatgtttctaatgg-tctgggt--gttttggtttgcgatcttctc-------------tgtgcagAGTGTTCTTGGGATTATTCTGGGAGGTGGAGCAGGCACGCGGCTCTACCCTCTTACCAAGAAGAGGGCGAAGCCTGCGGTTCCCCTGGGGGCGAATTATA

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------tttttagatcacaatagtttgaattt---tgatcttgtg---atatttgtattggatgt--ggattg---gttctggt-tctgattctg------attccaatttaaaatgttta-------tagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
                                                        ||| | | ||    | |||||    |     |||| | |   |||   |   | || ||  ||||      ||||  | |||||| ||       ||||  | | ||   ||||        ||||| ||  | || || || || || || || || ||||| ||||||||||||||||| || ||||||||||||||||| || || || || || |||||| 
gtgagtgcttgctctttcgcattgctgcattgtgggtttttttagcttgctttgcttttcttgctcgtt-tggtttggccatgcgcaatctagcggagataagggccgtagaagtccggatcatgcattcttttctctgatgctagaaaccattctcactgaagtggttttcttcttctagAGCGTTTTGGGGATCATTCTAGGTGGAGGAGCCGGGACACGGCTTTATCCACTCACGAAAAAGAGGGCAAAGCCAGCGGTGCCACTGGGTGCAAACTATC

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------------------------tttttagatcaca-atagttt----gaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgttta-------tagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
                                                                      |  || |  ||   | | | |    ||  |  |  |    ||  |  | ||      |   ||   |||| | ||       ||||  | | ||   ||||        ||||| ||  | || || || ||||| || || || ||||| ||||||||||||||||| || ||||||||||||||||| || || || || || |||||| 
gtgagtgcttgctctttcacgcattgctgcattgtgggttttttaccttgctttgcttttcttgctcgtttggttcggccatgcacaatctagcggagataagggccgtagaagtccggatcatgcattc-ttttctctgatgctagaaaccattctcactgaagtggttttcttcttctagAGCGTTTTGGGGATCATTCTTGGTGGAGGAGCCGGGACACGGCTTTATCCACTCACGAAAAAGAGGGCAAAGCCAGCGGTGCCACTGGGTGCAAACTATC

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|15337832|gb|BI498488.1|BI498488
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|10844760|gb|BF067973.1|BF067973
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|193679481|gb|FK621483.1|FK621483
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|120532534|gb|EH260667.1|EH260667
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|17022405|gb|BM093439.1|BM093439
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|9820051|gb|BE555564.1|BE555564
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|7796534|gb|AW781931.1|AW781931
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|209712745|gb|BW681599.1|BW681599
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|17400675|gb|BM177457.1|BM177457
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
EST: gi|23728291|gb|BU762193.1|BU762193
EST:     TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGA                         AGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA
genomic: TTTCTGATTCCCAAAACTCACAAACGTGCCTTGATCCCGATGCTAGCAGAgttcgtttac ... atgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
                           ttctgat  putative branch site (score: 3)
                                attccaatttaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttagatcacaatagtttgaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - -ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattcc