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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtcctatttcaatctacatacatacatacatacatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG

Basic information

species Glycine max
transcript GLYMA18G02210.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
------gtatatgtcctatttcaatctacata-cat-acatacatacatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
         | ||   ||      |    | | ||| ||| || |      ||  ||| | |  |  |||  || | | |   | ||   |   |   |||| ||| ||||||   | |||||||||||||||||| ||  |||||||||| ||||| || ||||| |||||| |   ||| || || |||||||| |||
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

upper sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 4
-----gtatatgtcctatttcaatctacatacat--acatacatacatacatacat-gatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
      | | |||   |  | ||   ||| |  |   || |  |   ||  |||||  || |   | ||  |     |      | |    ||   | |||| ||| |||||    | ||| |||||||||||||| || |||||||| |||||||| ||| |||| |||||  |||| |  ||  | || |||||||||
tgtgattttctgtttgacatgaactgacaaaattcagcaaaagtttgtatgtacattaattttggttttgatggacatgggtgggatttgttggtataagGGAGTTCAAGGAGAAGAGCAAGGTGGACAAGGTGGTGGTGCTGTGGACGGCCAACACGGAGCGGTACAGCAACGTGGTGGCCGGGATGAACGACACCATG

upper sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
---gtatatgt-cctatttcaatctacataca--tacata-catacatacatacatgatctgt-atcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
   || |  |   |||  | ||  |   |  |   ||||  |  ||    |||| | |||  | ||   |   | |   ||  ||| | ||   |  ||||| |||||||||    | ||||||||||||||| ||||| ||||||||||| ||||| || ||||| |||||| |   ||  || || || ||||| |||
atggtttggggatctagattaacatgattgaagcaacatggctcactggtatacgtaatccattatagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG

upper sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 4
gtatatgtcct----atttcaatctacatacatacatacata----catacatacatgatctgtatc-ttattcaggttctaactgttga---catgaactc---agGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
|||  |   ||    |   ||   |||  ||||| |  |  |       |  | |   ||  | ||  |||||        ||   | |    |||||||||   |||| ||| ||||||   ||||| || |||||||| || || || ||||| || ||||| ||||||||||||||  |||||| ||| ||||| |||||||||
gtacttaaactcaaaaacacagaatactgacataaacccgcaatggtgaattttccaaatgaggattgttattatcaactgaatcatggggttcatgaactctgcagGGAGTTCAAGGAAAAGACCAAGGTCGACAAGGTAGTCGTGCTATGGACAGCAAACACCGAGAGGTATAGCAACGTGGTTGCAGGGCTTAACGACACCATG

upper sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
gtatatgtcct----atttcaatctacatacatacatacataca---tacatacatgatctgtatcttattcaggttctaact---gttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
  | |||   |    || |  ||  || |   |  | | |||      ||    || |    |   |||   | | | |  ||   || |  |   |  ||||| |||||||||    | ||||||||||||| | |||||  |||||||||| ||||| || |||||||||||| ||   |  || || || ||||| |||
--acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagtataagtaatccattacagaagctatggcttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG

upper sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 4
gtatatgtcctatttcaatctacatacatacatacatacatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
|||   ||  | ||  | |    | ||||  || | || | |   |   |   | | |  | ||| | || |   |||    ||||  | |||| ||||||||| || ||||| ||||| |||||||| || ||||||||||||||||||||| | || || |||||| |||| || || ||||||||||| 
gtagtcgtaatcttcaatttcttaaacatgaat-cttaaaaatggaatgggcttttcttcttttctgattttgtatgt----atga--ttagGGAGTTTAAGGAGGCAACCAAGGTGGATAAGGTGGTGGTGCTGTGGACTGCCAACACAGAGCGATACAGTAATTTGATTGTGGGACTGAATGACACCATA

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|19270872|gb|BM887128.1|BM887128
EST:     GGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAA                         GGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
genomic: GGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAAgtatatgtcc ... atgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
EST: gi|120530232|gb|EH258366.1|EH258366
EST:     ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAA                         GGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
genomic: ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAAgtatatgtcc ... atgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
EST: gi|4296509|gb|AI442485.1|AI442485
EST:     ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAA                         GGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
genomic: ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAAgtatatgtcc ... atgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
EST: gi|6667615|gb|AW279066.1|AW279066
EST:     ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAA                         GGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
genomic: ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAAgtatatgtcc ... atgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
EST: gi|120530142|gb|EH258276.1|EH258276
EST:     ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAA                         GGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC
genomic: ATTAAGGGCACAAAGCAAGAGCAAGTTCAGCAAATCATCAAAGACATCAAgtatatgtcc ... atgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG
                  tatcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgtcctatttcaatctacatacatacatacatacatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG