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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgatattatcctcatcattgacacatttcttgtcatcttgtgtgtgctgcctgatatataggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG

Basic information

species Glycine max
transcript GLYMA02G08350.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g22950.3 (Oryza sativa), 3'ss of exon 1
---tttgatattatcctcatcattgacacatttcttgtcatcttgtgtgtgctgcctgatatataggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG
     ||||    |  ||    ||  || ||| |||    |    ||| |      |  | | | ||||    || |    | |||        |||    |||| || ||||| |||||||| || |||||||| || || |   | || || |||||||| |||||||||||||| || |||||||||||    || ||||
gtacatgattggttgttccaactttgcaaattgcttaa-gttggctgtatatcatttcttttgttggttagaattgca--ctgaatggttccttttttgacagGTTTGCGATGAGCTTGAGGACGTGATGGAAGAAGGTGGTATACTAGTAGATTACCATGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTTGTAGTTG

upper sequence: GLYMA02G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g22950.2 (Oryza sativa), 3'ss of exon 2
tttgatattatcctcatcattgacacatttcttgtcatcttgtgtgtgctgcctgatatataggtttatt-ttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCA--TGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG
                                                     || ||||   ||  |||   | |  | | ||||      ||||   |    ||   ||| ||||  | |||  |  ||   |        ||| || |  | |   || ||   |                                   
----------------------------------------------------gtggtatactagtagattaccatggatgtgatttc-----tttccagaacgttggtttgaccttgtagttgtgctccaaacagATAACTCAATTCTGCATGATCGCTTGACTAGCAG----------------------------------

upper sequence: GLYMA02G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G60340.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------tttgatattatcctcatcattgacacatt--tcttgtcatcttgtgtgtgctgcctgatatataggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG
                                                                     ||| ||  ||| | | | || || | ||  | |  | |   | ||  | |     ||   ||  |  |  ||  | |  ||   ||| |    |     ||||   |||||| ||||| |||| ||||  ||| || || |||||||||||||||||||||||||| ||||||||  |||| ||||||||| |||| || |
gttagtttcttactccatccctatccctttatcctccttatttccttgtcaacaaaacactttgaaccgttgctagaatcttaagc-ttcactctttagtttgataaagatttggattcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG

upper sequence: GLYMA02G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g03280.t01 (Vitis vinifera), 3'ss of exon 1
---tttgatatt--atcctcatcattgacacatttcttgtcatcttgtgtgtgctgcctgatata-taggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG
    |   | ||  || || ||| ||   | | ||   ||||       | |||  | | ||    |  ||| | | | |||    | ||||  |||||| || |||| || ||||| || |||||| | |||||||| |||||||||||||||||||||||||| ||||||||||| || ||||| ||||||||| | ||||| |
tatctcactgtttgatgcttatcttttgtagaattacagtcaatc---atatgcatcttaattccctttgttaaatcttcga---cattttgtgtggtttttgcagGTGTGCGATGAGCTCGAGGATTTGATGGAAGAAGGGGGAAACATTGTGGACTACCATGGTTGTGATTTCTTCCCTGAGCGATGGTTTGATCGTGTGGTGG

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|207771322|gb|GD746437.1|GD746437
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|298184959|gb|HO030172.1|HO030172
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|298172882|gb|HO019866.1|HO019866
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|298189345|gb|HO037748.1|HO037748
EST:     ATGATAGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|209726552|gb|BW662866.1|BW662866
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|298167337|gb|HO010776.1|HO010776
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|298177390|gb|HO027171.1|HO027171
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
EST: gi|7684843|gb|AW755491.1|AW755491
EST:     ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTG                         GTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC
genomic: ATGATGGATGGGATGATGAGCTTGATTGTCATGTTCTTAATGAAGACTTGgtaagatacc ... gtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctgcctgatatataggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG
                               gtttaat  putative branch site (score: 4)
                                              tttctgt  putative PPT
                   tttattttacgagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgatattatcctcatcattgacacatttcttgtcatcttgtgtgtgctgcctgatatataggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG

- - - - - - - - - - tgacaca
- - - - - - - - - - - - - - - cttgtca
- - - - - - - - - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - -tgcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcatg