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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtggctgttgatgtgatctgtttctttttttttttgtttagtatatttaattaaaaattgtattttctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG

Basic information

species Glycine max
transcript GLYMA20G22600.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22600.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 8
gttggtggct-gttgatgtgatctgtttct----ttttttttttgtttagtatatttaattaaaaat-tgtattttcttttta-cagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
|| ||| | |  ||||||      ||| |     |   | |    ||      | ||  || ||||| ||| ||   |||||  ||||||||||| ||||| ||||||||||| ||||| ||||||||||| ||||||
gtgggtagtttattgatgctggtcgttgcagaagtgcatctaaaattcttggaacttgctttaaaatatgtcttccatttttgtcagCCTCTGTTTCCTGGAGAGAGTGGAGTCGATCAGCTTGTTGAGATTATCAAG

upper sequence: GLYMA20G22600.3 (Glycine max), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------gttggtggctgttgatgtgatctgtttctttttttttttgtttagta-tatttaattaaaaattgtattt--tctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
                 ||||   |  |  |   ||   | |       |    | |   |||| |  | ||||  |     |  |   | |  || |||||||||||||| || ||||||||||| |||||| | || ||||| ||||||
accacatgtgtgtgtgtgttgcaagtcggagtcatggagtttgggcgagtgaggtggaggagtagtgctgaatttgacgagattctggatgtccttgcagCCTCTGTTCCCCGGAGAGAGTGGAGTGGATCAATTGGTGGAGATTATCAAG

upper sequence: GLYMA20G22600.3 (Glycine max), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------------------------------gttggtggctgttgatgtgatctgtttctttttttttttgtttagtatatttaattaaaaattgtattttctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
                                                                                                         ||  |||| || ||| ||||||  | |   |||  ||   |    |  |||   |    |    |    | ||  | |||||| |||||||||| || || |||||||||||| | || ||||||||||||
gtacttatgtagttcctggtagatggtgaattcatggagattctattactcctgagtactatggttcggaatggagatagatcattgtgttgattgtaatgagatgtaagtggttggtgaagtgatcattgttggtttagttagatgatatgaattctgtctggacaatttcgatgttggtgcagCCTTTGTTCCCTGGAGAAAGCGGAGTTGATCAATTGGTGGAGATCATCAAG

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|6566240|gb|AW233921.1|AW233921
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAT
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|22522569|gb|BU081380.1|BU081380
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|120495461|gb|EH223628.1|EH223628
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTANCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|12773850|gb|BG238777.1|BG238777
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|193629894|gb|FK575020.1|FK575020
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGT
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGT
EST: gi|15287684|gb|BI471575.1|BI471575
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|14990268|gb|BI315941.1|BI315941
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|27426708|gb|CA938228.1|CA938228
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|11413300|gb|BF425311.1|BF425311
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGNTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|192296530|gb|FG991636.1|FG991636
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAG
EST: gi|209699788|gb|BW655801.1|BW655801
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|15000029|gb|BI320843.1|BI320843
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|254333710|gb|GR848628.1|GR848628
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|192321549|gb|FK012899.1|FK012899
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGATGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|14990090|gb|BI315763.1|BI315763
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|11412139|gb|BF424159.1|BF424159
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|120492579|gb|EH220746.1|EH220746
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|22525150|gb|BU083970.1|BU083970
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
EST: gi|13481244|gb|BG510587.1|BG510587
EST:     TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAG                         CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
genomic: TTGACATCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTGCTTGGACAGgttggtggct ... ctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttttttttttgtttagtatatttaattaaaaattgtattttctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG
                       atttaat  putative branch site (score: 4)
                                    ttgtattttcttttt  putative PPT
     tttttttttgtttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtggctgttgatgtgatctgtttctttttttttttgtttagtatatttaattaaaaattgtattttctttttacagCCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA