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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaacttttgtatgtctagcattacctatgaataaactattcaatcttgtaaagatgtcccttcatagactttcactccttccttgtcttgcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG

Basic information

species Glycine max
transcript GLYMA10G32850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 2
ctaacttttgtatgtctagcattacctatgaataaactattcaatcttgtaaagatgtcccttcatagacttt-cactccttccttgtcttgcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG
                      ||  |   |      || |  ||   ||||  ||     |   |||| |||      ||   |||  | |  |   ||||||||| || |    ||||| ||||||||| ||  |||| ||||| |||||||||||||||||||||||    ||
---------------------gtaatttgaatctgtttacttgattgagtaatcataaagat---tagattttgtgaagctaagttgattggttttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG

upper sequence: GLYMA10G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 2
ctaacttttgtatgtctagcattacctatgaataaactattcaatcttgtaaagatgtcccttcata-gactttca---ctccttccttgtcttgcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG
     ||  ||    |    |  |   ||   |   | | |  | |||||    |||     |  || | ||| ||    |  ||| |     | |   || || ||  | |||| |  |||||  ||  |||| || ||| |  ||||||||||||||||||||||||||||||| ||
---ggttgagttaaacccatac-atgcatttgtctccaaatttaccttgtttgcatgattgcttgtatgtcttacaggtttttttcttcaatatccaattgcagATACATTAAAAACTTGATGGGTCTCTCTGGTCTCTCTATTCGAGAGGATGCTGTTGGTAACATATTTGGTCGATG
















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|120532605|gb|EH260738.1|EH260738
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|16347483|gb|BI973078.1|BI973078
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|298176989|gb|HO023350.1|HO023350
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|213595183|gb|DB960190.1|DB960190
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|209723482|gb|BW669483.1|BW669483
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|120532833|gb|EH260966.1|EH260966
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|298179399|gb|HO027870.1|HO027870
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGGGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|151408662|gb|EV278470.1|EV278470
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|209700349|gb|BW664386.1|BW664386
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|298171715|gb|HO021307.1|HO021307
EST:     CCACCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|120532878|gb|EH261011.1|EH261011
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|15338254|gb|BI498910.1|BI498910
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|193608632|gb|FK562378.1|FK562378
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|213616932|gb|DB959244.1|DB959244
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|209728923|gb|BW654990.1|BW654990
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|207808682|gb|GD780585.1|GD780585
EST:     CATCAGTAACCTAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CATCAGTAACC-AGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|193320687|gb|FK286530.1|FK286530
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|24205312|gb|BU964565.1|BU964565
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAA                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
EST: gi|209726738|gb|BW654840.1|BW654840
EST:     CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAG                         GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC
genomic: CCATCAGTAACCAGGGTCTTGTATACTGACAAGGATGTTTTAGGTCGCAGgtatatgtgt ... gcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtaaagatgtcccttcatagactttcactccttccttgtcttgcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG
                        ctttcactccttcctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaacttttgtatgtctagcattacctatgaataaactattcaatcttgtaaagatgtcccttcatagactttcactccttccttgtcttgcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - tgtatgt
- - - - - - - - - gcattac
- - - - - - - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - ctattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccttc