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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACAACAGATGATGTGCTTGCGGCCATTGACGGTGGTAAATCTGAAGGTGGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcctttctttttttttttctcaaaaaattcaatattctgtgtgtcgaagtttcataagtttctcttcctacaaaattggaatcttgttgcagc...

Basic information

species Glycine max
transcript GLYMA08G09180.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G63980.1 (Arabidopsis thaliana), 5'ss of exon 4
TAACAACAGATGATGTGCTTGCGGCCATTGACGGTGGTAAATCTGAAGGTGGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcctttctttttttttttctcaaaaaattcaatattctgtgtgtcgaagtttcataagtttctcttcctacaaaattgga-atcttgttgcagc------------------------
|  | || |||||| | |||   ||||||||| |||| | ||||||||||||| ||  ||| || |||||||| |||||||| || ||||| ||||||||||  || |     ||   |    |      ||| |  ||| ||||   |   ||       ||| |||       |    | |  ||  |  |||| | |                         
TGTCTACTGATGATCTACTTAGAGCCATTGACTGTGGAACATCTGAAGGTGGTCCAAATGGTCGACACTGGGTCTTGGATCCAATTGATGGCACTAAAGGgtacgttttaaaactaactagcct------aaagtcaaatcttcttatttcagagaaaatgtaaatttgatagaatgttgagtcagatgttatgttcctgacactgagcattttcatgattttag

upper sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 4
TAACAACAGATGATGTGCTTGCGGCCATTGACGGTGGTAAATCTGAAGGTGGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcctttctttttttttttctcaaaaaattcaatattctgtgtgtcgaagtttcataagtttctcttcctacaaaattggaatcttgttgcagc----
|| |    || ||||| ||| | |||||||||  ||||||||||||||| |||||   ||| |  ||||||||||||||||| || ||||| || ||||||||||  |  ||   |     |      |    |    || |  | | | ||    ||  |  ||| |       || |   ||    | | ||    ||    
TATCTGAGGAAGATGTTCTTACTGCCATTGACTCTGGTAAATCTGAAGGCGGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttggtta--tagaaatgcaacaatttgacatgatttcttatttatcttgcttctaccagtatgaaaa--tagatgtttatgttgtcgtgatggcatga

upper sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S83_223V6.2 (Physcomitrella patens), 5'ss of exon 4
TAACAACAGATGATGTGCTTGCGGCCATTGACGGTGGTAAATCTGAAGGTGGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcctttctttttttttttctcaaaaaattcaatattctgtgtgtcgaagtttcataagtttctcttcctacaaaattggaatcttgttgcagc------
| |  | ||| || ||  | |  ||||||||| | ||||| || ||||| |||     |||||| |||||||||||||| || || |||||||||| |||||||| |  | |    ||    ||||  | |    |   ||   | | |     | |||        | | |  | | |  | ||   | | ||| ||        
TGAGTAAAGAAGACGTATTGGAAGCCATTGACTGGGGTAATTCCGAAGGAGGTAGCAATGGACGCCACTGGGTTTTGGACCCCATCGATGGTACTAGAGGgtgagaaaacat---cttgacctttcagagactcctttgtagcttctcttcattattttagctgaagtgtgtgtcgatattaatgatttatggttccatgttttag

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|192323419|gb|FK015305.1|FK015305
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGGTCAATATGCTATAGCGTTAGCTTCACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|13311617|gb|BG405268.1|BG405268
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|21677711|gb|BQ630062.1|BQ630062
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTANAGG                         GTTTGTAAGAGGAGATCAATATGCT
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCT
EST: gi|207706660|gb|GD687502.1|GD687502
EST:     CACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: CACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|207787127|gb|GD756272.1|GD756272
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|208109287|gb|GD905787.1|GD905787
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|192311655|gb|FK004874.1|FK004874
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|193533228|gb|FK493706.1|FK493706
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|209712035|gb|BW674180.1|BW674180
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|192311684|gb|FK004875.1|FK004875
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAG-
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|193533912|gb|FK492049.1|FK492049
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|24205274|gb|BU964527.1|BU964527
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|208174050|gb|GD969089.1|GD969089
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|208165189|gb|GD965837.1|GD965837
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|7587871|gb|AW703678.1|AW703678
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAAGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|37996739|gb|CF808328.1|CF808328
EST:     TTCAGTTGGACGGCACTGGNGTTTTGGATCCGATAGATGGTACTANNAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAG
genomic: TTCAGTTGGACGGCACTGG-GTTTTGGATCCGATAGATGGTACTAA-AGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAG
EST: gi|193719481|gb|FK653521.1|FK653521
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|193556382|gb|FK514825.1|FK514825
EST:     GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGG                         GTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGG
EST: gi|6566797|gb|AW234429.1|AW234429
EST:     GGTTCAGTTGGACGGCACTTGGTTTTGGATCCGATAGATGGTACTAAATG                         GTTTGTAAGAGGAGATCAATATGCTATA
genomic: GGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcc ... gacattatagGTTTGTAAGAGGAGATCAATATGCTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACAACAGATGATGTGCTTGCGGCCATTGACGGTGGTAAATCTGAAGGTGGTTCAGTTGGACGGCACTGGGTTTTGGATCCGATAGATGGTACTAAAGGgtgagtatcctttctttttttttttctcaaaaaattcaatattctgtgtgtcgaagtttcataagtttctcttcctacaaaattggaatcttgttgcagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcttcc