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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

Basic information

species Glycine max
transcript GLYMA07G00430.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
atcatattttcccttataatgattaataaa---tttgtttggcctgtgctgcatg---agagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
     | ||||   || ||   | ||   |    ||| || |  | ||||  |||      |||||     | |     | |||   ||| |||| ||     ||||||| ||| | ||||| || ||  | || ||||| |||||||||||||||||||| |||||||| ||| | ||||| ||||| |||||||| || || ||
-----agtttcttgtagaacactaaaaggagtccttgcttagt-tatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgag-agttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
 |  | |  ||  ||  | || |  ||  ||||  | | |||    | ||| |  | |  |  || ||      | ||| | ||     ||||     ||||||| ||  ||||||||||||   | || |||||||| |||||||| |||||||| ||||| || ||  ||||||| || |||||||||||||| |||||
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaa-aatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
              | |   |    | | ||||  |  |    || || ||   | |    |  || |||||  |  | |  || |  | |||||| ||||||||||| | ||||| ||||||||||||||||| || ||||| |||||||||||||| || || ||  | ||||||||||||||  | ||||| || ||
----------gtaatgttcaggcacacagatttaat-agttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
--atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaat-tgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
    |||   |  | || |  || | ||  ||  | |||   |   | |   |     | || | | | |||||   ||   |  |  |  | |||| | |||| |||||| | || || || |||||||| |||||||| ||||||||||||||||||||||| |||||| | ||||| || || |||||||| || |||||
tttccattggtagcttttttttggtgaagcaacattttt---ccaagttttgtatatttattcaaaattattttctaaaccaatgtgatcatggaatgttcagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
-atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattg--cagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
  | |   |||   |  |  ||  ||  |  ||||| |  ||| || |    ||  ||  | | | |||| ||    |  ||||    || ||  ||   |||| |||||  ||||||| || || ||||||||||| || ||||| ||||||||||||||||| |||||| |||||||||| |||||||| ||||| || ||
cctgaagcttttagtggtcttgtctatcacctttgtgttacct-tgttatg-gaaggtgctgaga-tgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
-atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacact-----gatttt--gataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
  ||  || ||   ||||  |||    ||| |||   | ||   ||   | | | ||||| ||  ||     ||||||  | | ||   ||| | || |   ||||||| || || || || ||||| || || |||||||| |||||||||||||||||||| || || |||||| | |||||||| ||  |  | ||||| || ||
gttcccatcttgagttattctgaagcttaacttttgatcgca-atgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------atc-atattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
                                                      ||| | ||  |  || | |    || ||   ||  || |   | |     || |  |  |     ||   |||| |      ||||| ||||   ||||||| || || ||||| ||||| || ||||||||||| |||||||||||||||||||| || ||||| ||| | |||||||| ||  | || ||||| |||||
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------atcatattttcccttataatgattaataaatttgtttggc-ctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
                                         |||    || | | ||  |   |  || | |      || | ||| ||||  |  |  ||       |   ||    ||| || |||    ||||||| ||||| || || || || || || ||||||||||| |||||||||||||||||||| ||||||||| | ||||| || ||  | ||||| || |||||
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcat--acttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 11
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
                                 || || |||    | ||    ||  | | | ||||||||    |||               || |||| || ||  | |||||||||||  | || ||||| |||||||||||||||||||| || || || || |||||||| ||||| ||||||||||| || ||
---------------------------------gtatgtcct----tccaattcaggctcagcgctgattttatcgatg--------------gtttcagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 12
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
                                 || || |||    | ||    ||  | ||| ||||||||    |||               || |||| || ||  | |||||||||||  | || ||||| |||||||||||||||||||| || || || || |||||||| ||||| ||||||||||| || ||
---------------------------------gtatgtcct----tccaattcaggctcaacgctgattttatcgatg--------------gtttcagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

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|15813358|gb|BI785633.1|BI785633
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|192311315|gb|FK003450.1|FK003450
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGACTATTTTAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|192311314|gb|FK003449.1|FK003449
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
                                     ttctttttt  CT-rich tract
                      attttgataatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - ttccctt
- - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - - - - - - - tgcatga