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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaaacttagtcacagatattcattatatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA

Basic information

species Glycine max
transcript GLYMA09G30910.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------gtaagtttaaacttagtcacagatattcattatatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA
                                            ||    |  | |        |  |   |    ||| |   | ||||   | |||     |    ||   |||     || || ||||||||| |||||| ||||||||||||  || |||||||| ||||||  ||   |||  ||||| ||| |    || || || || || ||  || || ||||||
gtatgcagtaatcagttgtatccttctccagcttcagattcttctagcactgcattctactgacgtgaccaaactgataaattcagaagtaacataact-cataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G18070.2 (Arabidopsis thaliana), 3'ss of exon 6
-----gtaagtttaaacttagtcacagatattcattatatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA
      ||| | ||   ||  |  | ||  ||  |||  | |   |     |     |    |    | |  ||||   ||  | | ||| | |||||  ||||  | ||| | |||||||| |||||||| ||||||||| | || ||||||||  ||||||||||||| ||||||||| | ||  | || ||||
gtgagataaatatatgttttctt-ctgagttttgttaactctctctgatgattgcttagttgtctgattatgaatt---aatctaattttattcagGCACATTCAGAATGGTTATACAATGTCCCATGGGGAATGTACAAAGCTTTAATGTACATTGAGGAACGTTATGGCAACCCAACTATGATTCTCTCCGAAA

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtt-taaacttagtcacagatattcattatatatagatacaagtgca-acaaccatgcattgactaatttgtaagttcaat-ttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA
|| || | || ||||  | | |  | ||  || |      |   |  |  | ||||   ||  |    || |   |||      | | ||| ||||| | || | |||| | ||||| ||||||||||| ||||||||  | |||||||| || ||||||||||| || ||||| ||| | ||| | |||||||
gtgagatatacacttgattatatgtttttttttttccctaagcaatatatatacaa--gtgtctaagttattaaataaaccacttatcttatagGCTTACTCGTCTTGGTTATACAACGTACCATGGGGAATGTACAAGGCCTTGATGTATATGAAGGAACGTTACGGCAACCCTACTATGATCCTCTCTGAAA

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtttaaacttagtcacagatattcatta-tatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA
||||   | |  | |   | |  |||   ||| |   ||  || |  | ||      |||     || || |     ||   || ||| ||||| || |||| ||||||||||| |||||||||||| ||||||||  |  |||  ||| | ||||| |  |||||||||||| || | ||| | || ||||
gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttatg-----accaact-----gt---atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA

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|207719391|gb|GD703416.1|GD703416
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|208272871|gb|GE072313.1|GE072313
EST:     GAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: GAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|15812620|gb|BI784895.1|BI784895
EST:     CAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: CAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|12772704|gb|BG237640.1|BG237640
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|21887438|gb|BQ740651.1|BQ740651
EST:     GAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: GAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|23727814|gb|BU761942.1|BU761942
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTTGCTTTACAATGTACCATGGGG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGG
EST: gi|208189726|gb|GD992278.1|GD992278
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATT
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATT
EST: gi|193668309|gb|FK608529.1|FK608529
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|208328084|gb|GE119890.1|GE119890
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|209702643|gb|BW652738.1|BW652738
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|207785501|gb|GD755682.1|GD755682
EST:     CCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: CCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|209710516|gb|BW662052.1|BW662052
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|193342522|gb|FK306782.1|FK306782
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|208323136|gb|GE118291.1|GE118291
EST:     GGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: GGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|51335534|gb|CO979400.1|CO979400
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|208076553|gb|GD873956.1|GD873956
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGG
EST: gi|208080843|gb|GD873769.1|GD873769
EST:     TTGGTTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATT
genomic: TTGG-TCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATT
EST: gi|193732673|gb|FK668825.1|FK668825
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|58018438|gb|CX705180.1|CX705180
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|207769471|gb|GD742093.1|GD742093
EST:     GGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: GGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|208301945|gb|GE097425.1|GE097425
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGG
EST: gi|193602318|gb|FK558371.1|FK558371
EST:     CCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: CCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|207783519|gb|GD758053.1|GD758053
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|207833323|gb|GD804454.1|GD804454
EST:     GGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: GGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|208049627|gb|GD847032.1|GD847032
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCA
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCA
EST: gi|298165680|gb|HO008651.1|HO008651
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|14012034|gb|BG726965.1|BG726965
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGG
EST: gi|207813101|gb|GD785021.1|GD785021
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|192332518|gb|FK025623.1|FK025623
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACTATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|6727023|gb|AW311377.1|AW311377
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|207826830|gb|GD801075.1|GD801075
EST:     CCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: CCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
EST: gi|193677916|gb|FK616654.1|FK616654
EST:     ATGCAAAGAATGGAGTGCCTATTGGTCCTAGA                         GCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAATGGAGTGCCTATTGGTCCTAGAgtaagtttaa ... atttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA
                           gactaat  putative branch site (score: 2)
                                              tttttac  putative PPT
                              taatttgtaagttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttaaacttagtcacagatattcattatatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA