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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA

Basic information

species Glycine max
transcript GLYMA11G10330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaagatggctgggaatagaa----aataagcttctgtggaatttcttttcgttg--cagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA
     | |||  ||| | | || |||          |         |  || |  |||  || | ||    ||||  | ||| |     || | ||  |||  ||||| || || ||||| || || || ||||| ||||| ||  ||||||||||||| ||||||||||| ||||| |||||||||||  | |||||||| ||| 
-----tctgtttttaatat-cacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG

upper sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G105253_T03 (Zea mays), 3'ss of exon 3
------------------------------aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA
                               |    || ||   |    ||||||  ||| ||  || |  ||   |  | |    |   ||||   | |  | |||| || || ||          |||||||| || ||||| || ||||||||||| ||||| ||  ||||||||||||| ||||||||||| || || |||||||||||  ||||||| || ||| 
gtaaagcctgtgcaaagacaagtaaccacctacttattctggccaaaacacaattgataa-agtctttttctttcaattacacaaatcataatattcactttgtttctttgaaaatttcc-------cagGATGTTGGGCAGTCCATACTTGAAAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATATATGTTGATGATG

upper sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G158679_T01 (Zea mays), 3'ss of exon 4
-------------aatggtttgtgatta-gtgtacaattactaagaggattgtggttgggagaagatggct---gggaatagaaa--ataagcttctgtggaatttcttttcgttgc-agGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA
             ||       | |  | |       |  ||      ||     | |    |   |  ||    |  | | |||  | || ||||  |    ||  |    |||   |||||||||| ||||| || |||||| | || ||||| ||  ||||||||||||| ||||||||||| || || |||||||||||  | ||||| || ||| 
gtaaagctcatgcaaaaacaaataaccatggacttcttctctggccaaatcaaaatcgatcaagtctttctttcagttacacaaaccacaatcttcactttgtttcttgcgtgtttttagGATGTCGGGCAGTCCATACTTGAATGCTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATCTATGTTGATGATG

upper sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
aatggtttgtgattagtgtacaat-tactaagaggattgtggttgggagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA
    ||   | || ||| |  | | | ||  |  | |||   |   || | ||||  | |    | ||  ||||  | ||||    |||||      ||||||||| || || || ||||| || ||||| || || |||||||||||| ||||||| ||||| | |||||| || |||||||| || ||||| || ||| 
----gtacattat-agtttggagtgtgctttgctggttgca-tcatgaaacgatgcttag----ataatttaagagtttgtgtgtgttctt------gcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG

upper sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 5
aatggtttgtgattagtgtacaatta---ctaagaggattgtggttgggagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA
  | |||    ||| | |   |||||   ||     || |   ||||     | || | ||  |   || ||  ||||  | |     |     | ||| |||||||| || ||||| ||||| |||||||||||||| || ||||||||||| || || ||||||||||| ||||| |||||||| || |||||||| ||| 
gttagttcc--attggagaggaattaagcctcttgagaata-agttgctttgacatagatgaaagatgataaccagctcatttacttatctgcattgttacagGATGTAGGGCAGTCAATTCTAGAAAGTTATTCAAGGGTAATGGAGAGCTTAGCTTTCAACATAATGGCAAGGATAGATGATGTTCTTTATGTAGATGATG

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|193331420|gb|FK294644.1|FK294644
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTCGGACAGTCTATT
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgctact ... ttcgttgcagGATGTCGGACAGTCTATT
EST: gi|208089660|gb|GD886207.1|GD886207
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgctact ... ttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|193336303|gb|FK298119.1|FK298119
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTCGGACAGTCTATT
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgctact ... ttcgttgcagGATGTCGGACAGTCTATT
EST: gi|208051051|gb|GD848108.1|GD848108
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgctact ... ttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA
                                       tttcttttcgttgc  CT-rich tract
               aatagaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA

- - gtttgtg
- - - - - - - agtgtac
- - - - - - - - - - - - - - - - - - - -ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggctggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttctg