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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttctttctctggaaaacattattgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG

Basic information

species Glycine max
transcript GLYMA16G26850.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 3
-------tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttctttctctggaaaacattattgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG
       | |||  | |  |  |  ||| || |  ||||| ||  |||   |  ||||| |  |  |          |  | ||| ||  | |   |||||    ||||| | || || ||||| || || |||||||| ||||||||| |||||||||||||  | |||||||||||| | || |||||  |||||
catgttatttgtgatgactt-ctgcttataacat-ttatacttttttcctttgttgtacatgcacgtgacatatctaattatattctttatct---tgttta--cagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G340749_T01 (Zea mays), 3'ss of exon 2
tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttctttctctggaaaacattattg--ttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG
| ||  | ||  ||    ||   |    |  |||||  ||  | |  ||||  |   || |  | |||     || || | |    |   || |||    ||||| | || || ||||  |||||||||||||| ||||| ||| |||||||||||||  | || || |||||  | || || ||  |||||
tgtggttacagatggctcttgctatgactattatttgcttt-attgttgtaagtgc-ttgcaatatctaatgtaccttttggaccatgttatttttttacagGTTAGTGATTTGGAAAGCCAGATTGATAACTTCGAAGCAGAGATTGAAGGACTTTCAATTAAAAAGGGAAAACAAAGACCGCCTCGATTG

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------------tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttcttt----ctctggaaaa--catta-ttgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG
                                                                       | |  |   |||  | || |   || |    ||  |  ||||     | |  | || ||   |     |||| |   |  ||||| || ||||     |||   |||||  | ||  | ||    |||||||||| ||||||||||||| | |||||||| |||||||| ||||||||||  || || |||||||||
gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 4
--tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgt-acttatatttctttctctggaaaacattattgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG
  ||  | ||   |||  ||| |      || |   |   |||   || | | | ||| |||| |||   ||      | ||   | | |     ||||| |||| |||||||| |||   || ||||||| ||||||||||||  ||||||| || ||||| || ||||||||||  || || || ||| ||
gttccatgttacagtg--attgaattagtgtcaatctgttttcttttattttgagttaaattttttttcatgtggtttagtaacatgt-actgccttgagcagGTGGGGGAGTTGGAATCCCAAATTGATAGCTTTGAAGCTGAAATTGAAGGGCTATCTGTTAAAAAAGGAAAGACAAGACCACCTAGACTG

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|208297987|gb|GE095792.1|GE095792
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
EST: gi|209718497|gb|BW677667.1|BW677667
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
EST: gi|208218115|gb|GE016553.1|GE016553
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGGGAGTTAGAAAATCAGATTGATAA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAA
EST: gi|207846424|gb|GD819455.1|GD819455
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGGGA-TTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
EST: gi|213615319|gb|DB963513.1|DB963513
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
EST: gi|213616529|gb|DB967179.1|DB967179
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGNGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
EST: gi|208097464|gb|GD896363.1|GD896363
EST:     ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG                         GTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA
genomic: ATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTGgtatgaaatc ... gtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtacttatatttctttctctggaaaacattattgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG
                         aaaacattattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttctttctctggaaaacattattgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaac