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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaacattttactaataacacattctaatcattaaactctataaaaaaatatatatgccttaaataataatgtaattttttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC

Basic information

species Glycine max
transcript GLYMA05G37730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 3'ss of exon 2
taaaacattttacta-ataacacattctaatcatta--aactctataaaaaaatatatatgccttaaataataatg-taatttttttt---attttgtggtt-tatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC
       | |||||  || | |  |    |||||||   |    || |   |  | ||    ||||| ||  |    ||| |     |   ||||  ||||| |  ||||||| ||||||||||| || |||||||| ||||||||||||||  | || |||||| | |||||| | || || || |||||||  ||| | ||  || 
-------tattactgtatgataagtctacatcattagtgaggacatgattgagca-atggcacttaattacaagcactaactcccgctgcaatttgctggttctgcagTGGATCTTCTGGGTTGGCCCCTTCATTGGCGCTGCCCTTGCTGCCATCTACCACCAGGTGGTCATCAGGGCAATTCCATTCAAGAGCAGGTCGTAACCTG

upper sequence: GLYMA05G37730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 3'ss of exon 3
-taaaacattttactaataacacattctaatcattaaactctataaaaaaatatatatgccttaaataataatgtaattttttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC
 |||      | |  |    ||    ||  ||||   |   | ||      |  || ||||||   || | || | ||| ||||    ||||    |  |||||||||||||||||||||| |||||||||||||| ||||||||  |||| ||||||||||| ||| |||||||||| |||||||| || || |  |   
gtaagctccatgatcagacccaatcacttctcatctcatcatttatctg--tgaatctgccttg--tattgatttcattcttttg---ttgttcccttcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTACCACCAGATAGTAATCAGAGCCATCCCATTCAAGACCAGAGCCTGAGAAA

upper sequence: GLYMA05G37730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
------taaaacattttactaataacacattctaatcattaaactctataaaaaaatatatatgccttaaataataatgtaattttttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC
       ||||||||   ||| ||| |    | |||   |      | |    |  ||| | ||  |   |     || | ||||  ||  | ||||       |||||||||||||||||||||| |||||||||||| | || ||| |  |||| ||||||||||||||| |||| ||||| |||||||| || || |  |   
gtaagtgaaaacattgctcta-taagaagacccaatagcttc-tcatctcgtcatctatctgtgaatctgacttgtat-tgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA

upper sequence: GLYMA05G37730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 3'ss of exon 3
-----------taaaacattttactaataacacattctaatcattaaactctataaaaaaatatatatgccttaaataataatgtaatttt---ttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC
            |  | |    |  || || || |    |   ||  |  || | |      |  |  |  | |  | |   | | ||| |   |||| || | | | ||  ||||||| |||||||| ||||| |||||||||||||| ||||||||  |||| || |||||||||||| ||||||| || |||||||  |||||||  | | 
gtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctttgatggttaaattgagtttcagttcaagttcttattgtgactttttttctcttgctttcagTGGATCTTCTGGGTGGGACCGTTCATTGGAGCTGCTCTTGCTGCCATGTACCAGCAGATAGTCATCAGAGCCATTCCATTCAAGAGCAGGGCTTGAGATT

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|22930616|gb|BU547763.1|BU547763
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|207746543|gb|GD721530.1|GD721530
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|209706286|gb|BW680673.1|BW680673
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|207714331|gb|GD695852.1|GD695852
EST:     GGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|7284289|gb|AW596883.1|AW596883
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATTGGATGACCAA                         TGGATTGTCTGGGTTGGACCTTTCATTGGAACTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|209718916|gb|BW669105.1|BW669105
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|193438289|gb|FK401468.1|FK401468
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|151397692|gb|EV267565.1|EV267565
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTG
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTG
EST: gi|8826812|gb|BE210542.1|BE210542
EST:     TCTTCG-AGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGGTTG-ACCTTTCATTGGAGCTGCCCTTGCTGGTGTGTA
genomic: TCT-CGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGG-TTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTA
EST: gi|31466018|gb|CD408046.1|CD408046
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|31309774|gb|CD394977.1|CD394977
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|193428883|gb|FK392277.1|FK392277
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|208262601|gb|GE057583.1|GE057583
EST:     CATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: CATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|208132713|gb|GD927776.1|GD927776
EST:     GAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|193670308|gb|FK610276.1|FK610276
EST:     TCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGGCCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: TCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|58018784|gb|CX705526.1|CX705526
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|207683696|gb|GD665559.1|GD665559
EST:     ATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: ATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|10255191|gb|BE822957.1|BE822957
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|58019012|gb|CX705754.1|CX705754
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|31468418|gb|CD410446.1|CD410446
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|31466112|gb|CD408140.1|CD408140
EST:     GTCTCGGAGCTGCCATTATTTACTACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|151394316|gb|EV264187.1|EV264187
EST:     GTCTCGGAGCTGCCATCATCTACA-CAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|38192130|gb|CF921336.1|CF921336
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGGTGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|16343679|gb|BI969274.1|BI969274
EST:     GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
EST: gi|6726492|gb|AW310846.1|AW310846
EST:     GTTTCGGAGTTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAA                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT
genomic: GTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttct ... tggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatatatatgccttaaataataatgtaattttttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC
                               ttttttttattttgt  CT-rich tract
     tatatatgccttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaacattttactaataacacattctaatcattaaactctataaaaaaatatatatgccttaaataataatgtaattttttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC

-aaaacatt
- - - - - - - - -aacacat
- - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcct