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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgttgccttgtgctatactctttgtcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT

Basic information

species Glycine max
transcript GLYMA07G40350.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------aattgttgccttgtgct---atactctttgtcctgtactg--tagtgcatgtcaaacacacccatag--ttgtacagcattttgaact---tcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
                                                                            | ||| ||   |    |   | |  |  |      | ||   |||    | | |     |   || |  || | |       || |||   | ||| |||     |  ||||| |  |||| ||||| |||||||||||| | || || || || |||||||| || ||||||||||| ||||||||| | || |||||||| || ||||
gtacttttttctgatcattttatactgaactgtttttttattaaaatttaagtttaatggttcttaaacctttcaaagttggtgtgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT

upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 2
aattgttgccttgtgctatactctttgtcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
      |   ||   ||| | |      |||  |   | |   |   ||||         |||  |  ||  || | | | |    |||    ||  |||||  | ||||| || || || |||||||| ||| | |||||||| ||||||||| | || ||||| |||||||| ||||| || ||| ||||||||||||
-----gtaagttaatctaaatttgactgcctagatgatgga--agaccaaatgttttatcagtcttttag-gttgtaaccat----atgcgaattggcagGAACTGTTGGCTATACAGCAACAAGGACCAAGAACAATTGGCTTCTTTGGAACTAGAAATATGGGTTTCATGCATCAAGAGCTCATTCAGATTCTTAGCT

upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0042g00120.t01 (Vitis vinifera), 3'ss of exon 1
aattgttgccttgtgctatactct-ttgtcctgt---actgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
     |       |   || |||| |||     |   |      ||| |  |     |  | |   |  |   | ||    |  || ||| | ||  ||| |||||||||||||||||||||||  |||| || |||||||||||||| ||||| || || || ||||||||| |||| |||||||| || ||||| || ||||
--ccataattccatatgattctctgttgcaacatggaagcaccctgctttcccctttctgctaatttctttgggtatgcctatatttattttatt--tttgcagGAGTTATTGGCCATTCAACAAGAAGGGCCAAGAGCTATTGGCTTCTTTGGGACACGAAATATGGGATTCCTGCATCAAGAACTTATCGAGATCCTGAGCT

upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 3
aattgttgccttgtgcta-tactctttgtcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcat-tatg----tttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
    |||||  || || |  | |||  ||  |   || |        |   |   ||   |  ||||   | ||||| || ||  | | ||    ||  ||| ||||||||||||||||| ||||| ||||| || ||||||||||| || ||||| ||  |||| ||||||||||  || |||||||| ||||||||||| ||||
---agttgcaatgagcaagcattctaggttttcccctttctattgatttttatgaacatcttattgt---ggattttaaagttgctatgtgcgaattattttgcagGAGTTATTGGCCATCCAACAACAAGGGCCAAGAGCTATTGGGTTCTTTGGGACAAGGAATATGGGATTCACACATCAAGAACTTATTGAGATTCTCAGCT

upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S134_28V6.1 (Physcomitrella patens), 3'ss of exon 2
---aattgttgccttgtgctatactctttgtcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
      | || |   || | |       || | | |  |||  ||||   |       |   |   | |   | |   || ||  |  |    |  ||| |||||| |  | || ||||||||| | ||||| || ||||| |||||||||||||||||||||||||| |||||||||||  |||| |||||||||||||| |
gagggctttttcaaggttcaaattctaatgacttat-ttgtgttgcactacgttttggcttgtttcttttatgaacgatgcacacc--tgctgtggttttcagGAGCTTCTAGCAATTCAACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTT

upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 2
-aattgttgccttgtgctatactctttg-----tcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
 |  | ||     |  | | ||| || |     |  ||  ||| | | | | |    |       |  ||||  |  |  |  | || |    ||| | ||| |||||| |  | |||||||| ||| | ||||| || ||||| || |||||||| |||||||| ||||| |||||||||||  |||| |||||||||||||| |
aaggttttatgaagatcaagacttttagggtgtttgtgcgctgcactacgtatttggcttgtttct--ttgttaacaagctacagctgc----tgtgttttttcagGAGCTTCTAGCCATTCAGCAGAATGGACCAAGGGCTATAGGGTTTTTTGGTACTCGGAATATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTT

upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ38716 (Selaginella moellendorffii), 3'ss of exon 1
aattgttgccttgtgctatactctttgtcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttcttta-cagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
                ||   |||| || || |   | |   | |||    |     | | ||| | | | | ||   |  |  || | || ||||  |||||  |  | || || ||||| ||||| || |||||||| ||||| || ||||| || ||||||||||||||||| ||| | || |||||||| ||||| |
---------------gtaagttcttagttctct--cgaaactcttgtt--ccttcttctttgtttttcgggagttcttatgtttttctcttcctttctcagGAACTTCTCGCGATCCAACAACAAGGGCCAAGAGCTATCGGCTTCTTCGGAACGCGAAACATGGGATTCATGCATCAACAGCTTATTGAGATACTTAGTT

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|151398252|gb|EV268130.1|EV268130
EST:     CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAG                         GAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
genomic: CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAGgtttgtaaca ... ttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
EST: gi|15664820|gb|BI702191.1|BI702191
EST:     CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAG                         GAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
genomic: CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAGgtttgtaaca ... ttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
EST: gi|31466950|gb|CD408978.1|CD408978
EST:     CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATCTTGATCATCTGCAG                         GAGTTATTGCCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
genomic: CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAGgtttgtaaca ... ttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
EST: gi|193455573|gb|FK420978.1|FK420978
EST:     CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAG                         GAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
genomic: CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAGgtttgtaaca ... ttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
EST: gi|19348270|gb|BM892802.1|BM892802
EST:     CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAG                         GAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA
genomic: CCATTCGCGTAGCGGAGTTCAAGCCTGTTCCTGATGTTGATTATCTGCAGgtttgtaaca ... ttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT
                                          tgtttcttt  CT-rich tract
                                      attatgtttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgttgccttgtgctatactctttgtcctgtactgtagtgcatgtcaaacacacccatagttgtacagcattttgaacttcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC