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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccttacctcaacaaagaaagtgtggtaagtggcaacacacgtgttgcatttttggcccagcaataacacgtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC

Basic information

species Glycine max
transcript GLYMA02G39230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
taccttacctcaacaaagaaagtgtggtaagtggcaacacacgtgttgcatttttggcccagcaataacac-gtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC
||      ||| | |       |    |   |        | ||  ||| |       |    ||||   | |    | ||      || |  ||   ||||||||||| ||  |  | |||||||| || || |||||||| ||||| || |||||||| ||||| ||||||||||||||||||||||| |||||||| |
tatgagcactctatacttcctct-cactctatacttcattaagttctgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC

upper sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g01370.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------------------------taccttacctcaacaaagaaagtgtggtaagtggcaaca----cacgtgttgcatttttggcccagcaataacac-gtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC
                                                                                    | | ||     ||     |  |    | | |    ||      | ||  ||| |       |    ||||   | |    | ||      || |  ||   ||||||||||| ||  |  | |||||||| || || |||||||| ||||| || |||||||| ||||| ||||||||||||||||||||||| |||||||| |
gtatatcttttttctgtattgattggatcatagtttttccagaataaagcatgaaaagttgctgtaggttattgagttgggtgcagcctatgagcactctatacttcctctcactctatacttcattaagttctgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC

upper sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------------------taccttacctcaacaaagaaagtgtggtaagtggcaacacacgtgttg-------catttttggcccagca-ataacac---gtgtttttgtggt----gtactaaaatgga-cagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC
                                                                || ||     |  |||  ||| |    |    ||   ||  | || ||       ||||||  |   |    |||   |    || ||| || ||     |  |   ||||| ||||||||||| ||| || |||| || || || || || |||||||||||||| ||| | || ||||| |||||||||||||||||||||||||| || ||||
gtactgataaacaaagatatggtcagaacactaatttgagttcttggattcttaacttgatggttagctgcagcctgcaaccaaaatagatttcaggggtccaaccttgctgagaagtacattttatgtagaatggatagagcctaatgctttagttgtcattatgttggtatggaacagGAATGGAGCTATCTACGAGGAGGGCTAACAACGGTTGATCGTGACTATGGCTGGTTTAACAACATCCACCATGACATTGGCACCCATGTTATACATCATC

upper sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g06720.t01 (Vitis vinifera), 3'ss of exon 7
----------taccttacctcaacaaagaaagtgtggtaagtggcaacacacgtgttgcatttttggcc-cagcaataacacgtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC
          |  | | ||       | |||  |   ||| |  | ||     | || | | |||  |  || | | ||    ||| |||||| ||         | |||||||||||| ||||| || || || || || || || |||||||||||||| ||| | |||| ||| || ||| ||| |||||| |||||||| |||||||
gtactgataattgcatcccctgctcgacaaaaagccttaaatt-ctacttggatttttcttgtttaactgcaactagaatggatgtctttgtg-tg---------gaacagGAATGGAGCTATTTGAGGGGAGGGCTAACGACGGTTGATCGTGACTATGGATGGTTTAATAGCATCCAACATAACACTGGCACGCATGTTATACACCATC

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|58014509|gb|CX701251.1|CX701251
EST:     ACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAG                         GAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGT
genomic: ACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAGgtaacaaaaa ... aaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGT
EST: gi|151407473|gb|EV277288.1|EV277288
EST:     ACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAG                         GAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGT
genomic: ACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAGgtaacaaaaa ... aaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGT
EST: gi|208219374|gb|GE020164.1|GE020164
EST:     ACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAG                         GAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGT
genomic: ACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAGgtaacaaaaa ... aaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatttttggcccagcaataacacgtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC
                                        tactaaa  putative branch site (score: 1)
                                        tactaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccttacctcaacaaagaaagtgtggtaagtggcaacacacgtgttgcatttttggcccagcaataacacgtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC

- ccttacc
- - - - - - - aaagaaa
- - - - - - - - - - -gtgtggt
- - - - - - - - - - - - - - - - - -aacacac
- - - - - - - - - - - - - - - - - - - -cacgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg