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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 12
gtatactgctattcaatatttttaagcatgaaaatacttgatggc--gacttttagacat-gtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
                     | ||  || |||||  | | | ||  || ||||  |  |  ||   || | |  |||  |  |        ||||| || || || |||||||| ||||| ||||| |||||||||||| | || ||| |||||||||||||||| ||||| ||||
--------------------gtaaaatattaaaatcttggtttgcaagatttttgaatgtcatataaatctgacataaaaaa-accatgtttcagGTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaatta--tttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
                     | ||| || || |   | | | || |  ||| ||    ||  ||  | |||  |||  |  ||       ||||| || || || ||||| || ||||| ||||| |||||||||||| | || ||| |||||||||||||||| ||||| ||||
--------------------gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtt---tcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
||| | ||  |      |  ||     ||  |  | |||     | |  |  | | || |||||   ||  |  ||||  ||   | | ||||| || || || |||||||| ||||||||| | |||||||||||  | ||||| || ||||| |||||||||||||| ||||
gtaca-tgtcaccgtgcaacttc---tatccagcttcttttctcctaactacata-atttaatttcatatctctattaa-atcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
gtatactgctattcaatatttttaagcatgaaaatacttgatg-gcgactttta-gacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
|||| ||| |   || | || |||          | | | ||   | ||   || || | | |   ||||   ||| | | | |||||  ||||||||| || || ||||| || |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| ||||
gtatcctgtttcaca-ttttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttg--ttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 11
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
                                        | |    || ||   | ||   |  |  |      |   | ||      |||||||| || || |||||||| ||||| || || |||||||||||  | |||||  ||||||||||||||||||| || || |
-----------------------------------gtgataggattgctcttgttcttgctttcctacacacgcgtacatgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 11
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaattattta-atttaattat-tattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
                                      |||| |    | |        |  ||   || |      ||  | ||      |||||||| || || |||||||| ||||| || || |||||||||||  | |||||  ||||||||||||||||||| || || |
-------------------------------------gtgataggatttctcttgttcttgctttcctacacacgcgtacatgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

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|17154046|gb|BM143979.1|BM143979
EST:     CTGCTGCCCTGGATGTTGTTGCCAAACATCTGAATTTGAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
EST: gi|16349332|gb|BI974927.1|BI974927
EST:     CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
EST: gi|27426004|gb|CA937524.1|CA937524
EST:     CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
EST: gi|193450026|gb|FK412580.1|FK412580
EST:     TGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGTAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: TGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTG-AAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
EST: gi|208099059|gb|GD893926.1|GD893926
EST:     TAGCCAAACATCTGAATTTGAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: TAGCCAAACATCTGAATTTGAAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
EST: gi|13312878|gb|BG406529.1|BG406529
EST:     CTG-TGCCCTGGATGTTGTTGCCAAACATCTGAATTTGAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
EST: gi|7458620|gb|AW666070.1|AW666070
EST:     CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAG                         GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
genomic: CTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAGgtatactgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatggcgacttttagacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
                                atttaat  putative branch site (score: 4)
           ttttagacatgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA