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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaacaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG

Basic information

species Glycine max
transcript GLYMA10G30900.2
intron # 3
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 3
lower sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
ctaaacaaacttaacgtttattatttaagtgtttgtg-gtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgact---agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG---
     |   |     |||| |||| |     | |||        ||| ||  | ||| |   |       |   | |||   |||  |||| | |  ||   |||||||  |||| ||| | ||||| ||||||||||| |||||||||||||||||| | || ||| ||||||||||||| ||  |||||||||||||||   
--cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccataattt--gtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g45240.4 (Oryza sativa), 3'ss of exon 2
ctaaacaaacttaacgtttattatttaagtgtttgtg-gtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgact---agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
     |   |     |||| |||| |     | |||        ||| ||  | ||| |   |       |   | |||   |||  |||| | |  ||   |||||||  |||| ||| | ||||| ||||||||||| |||||||||||||||||| | || ||| ||||||||||||| ||  |||||||||||||||
--cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccataattt--gtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
-ctaaacaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
 ||| |   | | |   ||   |   | | ||  ||  |  | ||   | | || |  ||| |  | |   |  | |||    |     | | |     ||||||| ||||| ||| ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||  ||  | ||||| |||||||
tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcatgcattttt-tgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 2
--ctaaacaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgact-agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
  ||||  |  |    | | | | | | |  ||| ||  |    ||   | | || |  ||| || | |   |  | |||    | ||      ||   | ||||||| ||||| ||| ||||||| || || |||||||||||||||||||||||| | || ||| ||||| | ||||  ||  | ||||| |||||||
ctctaagtag-cgaggcttatgtcagtcat-tgtgtgcagcatttggcatgcatt-tcttgattttatacattcttaatttgcctttgcactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAGACTAAAGGTTATGGATTTGTGAGCTTTTCAAACCCTACTGACTTGGCTGCAGCAATAAAAGAGATGAATG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
--ctaaacaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtat-gtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
      |  |   | ||    || |   |  |   | |   |  |   |||  | ||    |  |   |        || |  || |  |||| | |||| ||||  | ||||| ||||||||||||||||| || |||||||| |||||||| ||    |||||| | || || || |  ||  | |||||||||||||
atacggatcattcttactcgaatcacaaagataagtattcagtgttagttttgtggt--caaactcgtaccagaaaaataagagtcttatttaccatgac-agGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGTTTCTTAAATCCTGCGGATCTAGCAGCAGCCTTAAAAGAAATGAATG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 3
ctaa-acaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgact---agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
 ||     | |||   |  |     |||| | ||||   ||      | || |   | |   || |  || | |  | ||| | ||  ||      |||   ||||||||||||| |||||||| || ||||| |  || ||||||||||| |||||| |||| ||||  |||||||| |  || ||||| |||||||| |
ttactgtgatcttgcaggctggctgttaattttttg-aatgaggacttgtcatatcactt--tttatggt-tggaaactaatgcatagttcctcacactcacagGTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTATGGATTTGTTAGCTTTTCCAACCCTTTAGACCTTGCAGCAGCACTTAAGGAAATGAACG

upper sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 3
ctaaacaaacttaacgtt---tattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgact---agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
   ||      | |  ||   | |   |||| | ||||   ||      | || ||  | |   || |  || | |  | ||| | ||  ||      | |   ||||||||||||| |||||||| || ||||| |  || | ||| ||||| |||||| |||| ||||| |||||||| |  || |||||||||||||| |
---aattgctgtgatcttgcatgtctgttaaatatttggaatgaggacttgtcatttcattt--tttatggt-tggaaactaatgcatagttcctcacattcacagGTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG

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|14009094|gb|BG725698.1|BG725698
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGTAAAACAAA
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAA
EST: gi|22523081|gb|BU081892.1|BU081892
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
EST: gi|254348659|gb|GR852338.1|GR852338
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGGTAAAACAAAAGGTTATGGGATTTGTGA
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGG-TAAAACAAAAGGTTATGG-ATTTGTGA
EST: gi|15664653|gb|BI702024.1|BI702024
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
EST: gi|193355864|gb|FK323473.1|FK323473
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
EST: gi|207809104|gb|GD781738.1|GD781738
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
EST: gi|6341837|gb|AW164661.1|AW164661
EST:     ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA                         GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC
genomic: ATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggt ... tcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG
              agttgac  putative branch site (score: 4)
                                         tttatctt  putative PPT
                                     tatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaacaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA