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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgtgttaatgggtatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtgggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA

Basic information

species Glycine max
transcript GLYMA02G09140.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g06520.1 (Oryza sativa), 3'ss of exon 1
-agttgtgttaatggg----tatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtgggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
 |  || | ||   |     |   ||  |||||    || |||    |  |  | || ||  |    |||| || | ||    ||| |||   |   |  ||||| ||||| || |||||||| || |||||||| |||||||| ||||||||    ||||| || ||| ||||||||||||||||||| || ||||| || || 
gatctgggctatctgtgccttgcttgatttgtgatgtaattggggagatgtattggggcttgt----tgat-ttaggttaagcttgtgatggcgcttgtgtgcagAATTCTGGCGAACAGGCAGTCGGCTGCAAGGTCCAAGGAAAGGAAGATCAAGTACACTAGCGAGCTGGAGAGGAAGGTGCAGACACTGCAGACCGAGGCC

upper sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 1
-----agttgtgttaatgggtatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtgggct-tgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
      | ||   || || |  | |   |  |        |    ||||  |       || |||  |     |   || |||   || || | |    | || |||||||| || ||||||||||| || || || || ||||||||||||||    |||||  ||||| ||||||||||||||||||| || ||||| || |||
gaagttgctggcctattgtgcttcttcttcttctttt--tttcctgaaatcgggctccttgttgcgtt----ctcaatttgatggtgggtactctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA

upper sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G821024_T01 (Zea mays), 3'ss of exon 1
--agttgtgttaatgggtatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtgggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
         |   |     | | |   || | |   ||    |   | |   ||| | |    ||| | | |   |||   | |  |  |   |   |||||||| || || ||| |||| ||||| || || |||||||||||||||||    ||||| |||||| ||||||||||||||||||| || ||||| || || 
gtttcaagatccgtatccttgtcgcgcgttgaatttcttctggtccaagtgaggtgtaactatctggtttcgcggtggtcctcgactcctc--gttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC

upper sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G079365_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------agttgtgttaatgggtatatggattg--tgggaaaactggaagaaaatgattggtctga--tgcactgatattggcttggatttggg-ata----------ttgtgggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
                                           | |||  |     | |   ||   ||  |     | |||| |    ||   | |||     ||  |   |  ||| ||  |  | || |||            | ||   |||||||| || || ||| |||| || || || || |||||||||||||||||    ||||| |||||| ||||||||||||||||||| || ||||| || || 
gtgagcaaacgccttcagcgtccgcgagctgtcttcaccttggaattgcttcccccgctgcttgagatgcttcatggagctgggacgtgataccttgtcctgcctggtcaagtcctggtttcaagataggtataatttcctctcccgcggcggtgcagGATCCTGGCGAACCGGCAGTCCGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC

upper sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G43700.1 (Arabidopsis thaliana), 3'ss of exon 1
agttgtgttaatgggtatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggat--attgtgggctt---gcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
   | | | | |  || | ||  || |      |||  |||    | | |  | || ||   ||||   || ||| | | | | |   |  |||| ||     |||||| | || || || |||||||| || || || || |||||||||||| | || ||  ||||||| ||||||||||| ||||| ||||||| |||||| 
--gtatataatttagtgt-tgtttttt------acttaaagcttgtaacttttttg-tgatttgattgaggtttgaaatagtgttttgtgatgggtttttgatagGATTTTAGCGAATAGACAATCTGCGGCGAGGTCGAAAGAGAGGAAGATTAGGTATACTGGTGAGTTAGAGAGGAAGGTTCAGACACTTCAGAATGAAGCT

upper sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0076g00330.t01 (Vitis vinifera), 3'ss of exon 1
agttgtgttaatgggtatatggattgtggga-aaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtg--ggcttg--cagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
  ||| | |||  ||   ||    | ||    ||  |         ||||     |||     |||| | | |    | |    ||  |  |   |||||  |||||||||||| || || |||||||||||| | || ||||||||||| || || || || | |||  ||||||||||||||||||| |||||||| ||||||
--ttg-gctaagaggagcatttgatctgaattaagttattcaggggtgatcatcttgagtt--tgatctggacaactaatgttaattctaagctagcttgagcagGATTCTTGCAAATAGACAATCTGCTGCACGTTCAAAGGAGAGGAAAATACGCTATACTAATGAACTGGAGAGGAAGGTGCAGACACTTCAGACAGAAGCA

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|120492184|gb|EH220351.1|EH220351
EST:     CCTGATAAACTTGCTGAACTTGCTCTTATGGATCCCAAGAGAGCTAAGAG                         GATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCG
genomic: CCTGATAAACTTGCTGAACTTGCTCTTATGGATCCCAAGAGAGCTAAGAGgttctttttc ... gggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCG
EST: gi|21888328|gb|BQ741541.1|BQ741541
EST:     CCTGATAAACTTGCTGAACTTGCTCTTATGGATCCCAAGAGAGCTAAGAG                         GATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCG
genomic: CCTGATAAACTTGCTGAACTTGCTCTTATGGATCCCAAGAGAGCTAAGAGgttctttttc ... gggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCG
EST: gi|16342552|gb|BI968147.1|BI968147
EST:     AGAGAGCTAAGAG                         GATTCTTGCTAACANNNAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCG
genomic: AGAGAGCTAAGAGgttctttttc ... gggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCG
EST: gi|21888384|gb|BQ741597.1|BQ741597
EST:     CCTGATAAACTTGCTGAACTTGCTCTTATGGATCCCAAGAGAGCTAAGAG                         GATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGA
genomic: CCTGATAAACTTGCTGAACTTGCTCTTATGGATCCCAAGAGAGCTAAGAGgttctttttc ... gggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattggtctgatgcactgatattggcttggatttgggatattgtgggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
              cactgat  putative branch site (score: 3)
                 tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgtgttaatgggtatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtgggcttgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
agttgtg
- - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttg