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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG

Basic information

species Glycine max
transcript GLYMA15G02400.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 8
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctat-acttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
                                        |  || |  ||| |  |||  || |        | |  ||  | ||| || |  |||| |  |   |||| |  ||||    |   |  |||| ||||||| |||| |||||||||||||||| ||||| ||||| ||||| ||||| ||| |||||||||| ||||| | |||||| |||||||| || |
----------------------------------------gtaatgatctttttcacattatatt-------gacattagggtatgaatt-atggtgt-atatgcataatttgtttctaccctatgtgcagGTAATTGACAGATCATTTGGTTTCGACACTGCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagttta-aagtgtcacctatttaatgtcatt-ctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
                      | | | | | |  | |||    |  | || ||       |   | |||   | |    |  |||    |  |   |    |     |  ||| |  |     || || |||| |||||||| ||| ||||||||||||| || ||||| ||||| ||||| ||||| ||| |||||||||||||||| | ||| || |||||||| || |
--------------------gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G443985_T03 (Zea mays), 3'ss of exon 8
gtaa--tgatgcttta-gttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
||||  || | ||  |  || ||      | | |||| |||     |       |||||||   ||  ||    |  || |      ||     |  || |    ||| |  || |  |      || || |||| |||||||| ||| ||||||||||||| || || || ||||| ||||| ||||| ||| ||||||||||||| || | ||| || |||||||| || |
gtaatatgtttctccacattttagtgacatttttgtgtaaaaatggaag-----atgccatttgacatgatcacatgaacaa----cgaaccccatatg-cgtgaattcaccgttaccca-----tgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaag-tgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG------------------------------
                                                                                      |   | |  |||    |  | | | |   | | ||| || || ||||||| ||||| ||| ||||||| || |||||||| ||||| || || || || || ||| | ||||||||||||||   ||| || || |||||||| |                              
--------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgtatatatatggtt-aggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
gtaatgatgctttagttgtaaaattgtatatgtggaaattgct---atacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
|||||  |     | || ||    | | | | |  |  ||||    || |||||    |||    || ||   | || |  | | |  ||    |  |||    |  | | | |   | | ||| || || ||||||| ||||| ||| ||||||| || |||||||| ||||| || || || || || ||| | ||||||||||||||   ||| || || |||||||| |
gtaatttttggccacttctacttgt-tctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcaga--gacctgtactatgctgattatttgtatatatatggtt-agGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 8
--------gtaatgatgctttagttgtaaaatt---gtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
         | |  |  | ||   | | | |||   | |  | | ||||       |   || |   |||  | ||  ||     |  ||| |||| |   ||||    |   |||| |       ||| | |||    ||||||| ||||||||  |||| || || || ||||||||||| ||||| || ||||||||| |||| ||||||||||| || ||     | ||||| ||||
gtaggtttctgacaaatccttgagtctgatattcgtgcaactctcgaaagaatcgaa---ttgtatgatca-agtcttaattgggaccagactttgtgaggaaagacgaattgatttgac------ctggaattgg--cagGTTATAGACAAATCGTTTGGGTTTGATACAGCTGTTGAAGAAGCACAGCGCGCAATCAATGCTGCCCATGTGGAAGCTGAGAGTATTCACAATGGCATTG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaat------gtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
||||||      |  | ||| ||   |  |  |     || ||| || |   |||   | ||      | ||  | |  |    |    | |  | |   |    || |      || | |  |   |      || | ||||| || ||  | || ||||||||||| || ||||| |||||||||||||||||| | |||||||||||||| || ||  |  | |||||  | |
gtaatgtgctccttatagtacaacacttgaatttttttttactacacatgcttgcgtgcttatgtcgcatgatgatagcatcccgttgcttatatattgacctcctagtccttgggttacttggagatgagagcagATAATTGATAAGTCCTTCGGGTTCGACACTGCCGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTACTCATAATGGTGTGG

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatt---tagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
||| | || | | |    ||    |  | |         |  |  || | | |||     | | |     |    ||   |||   || |    | | || | ||   | |     | | ||| | |    || | ||||| || ||  |||| || ||||||||||| ||||| |||||||||||||||||| | ||||||||||||||||||||  |  | |||||  |||
gtact-atacatcatcccta---ctacacagtgacgcgctttttcacatgtgtgcttatttccacatgttgcctgaattcattc--gtgtgcgttctgacttgttctcttttgggatttgtttcaatgaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG

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|151400140|gb|EV269954.1|EV269954
EST:     TGAAAGTTGCAGTGGTCGGAATTCCAAAAACTATTGACAATGATATCCCA                         GTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGA
genomic: TGAAAGTTGCAGTGGTCGGAATTCCAAAAACTATTGACAATGATATCCCAgtaatgatgc ... tttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGA
EST: gi|8283061|gb|BE020622.1|BE020622
EST:     TGAAAGTTGCAGTGGTCGGAATTCCAAAAACTATTGACAATGATATCCCA                         GTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGA
genomic: TGAAAGTTGCAGTGGTCGGAATTCCAAAAACTATTGACAATGATATCCCAgtaatgatgc ... tttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGA
EST: gi|151406712|gb|EV276527.1|EV276527
EST:     TGAAAGTTGCAGTGGTCGGAATTCCAAAAACTATTGACAATGATATCCCA                         GTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGA
genomic: TGAAAGTTGCAGTGGTCGGAATTCCAAAAACTATTGACAATGATATCCCAgtaatgatgc ... tttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
                          tatttaatgtcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA