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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgatgttcctattaatatcatccatgatcttgcaggttatggtaattttagtgaaaatacatttgactgatttgatctttgtcatcttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT

Basic information

species Glycine max
transcript GLYMA09G02160.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 3'ss of exon 3
tctttgatgttcctattaata-tcatccatgatcttgcaggttatggtaattttagtgaaaatacat-ttgactgatttgatctttgtcatcttgtatt-tagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT
     |  || | ||  | ||   |   |  |   | ||| | |    || |  |  ||    |||| |  | || |      ||| |  |||   |||  |||||||| |||| || || ||| | ||||| |||||||| |||||||||||||| ||  | ||||| || |||||||| |||||||| || |||||||| |
-ggagggagtacatagcagtagctagtaaaaaaaatccagatga--acaaataaacggatttaacatatcaattggtacttattttatggtctgtcattacagGTTCTTTTGAGCCGGTTAAGGCTCTTCTTAAGTCCTGGTTATCCATATGAAGAGATCCTCAGGACATTCCACAATCAAACAAGCATTATTATGTGCTCTT

upper sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G003379_T01 (Zea mays), 3'ss of exon 3
tctttgatgttcctattaatatcatccatgatcttgcaggttatggtaattttagtga-aaatacatttgactg-atttgatctttg--tcatcttgtattt-agGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT
  |  |  | ||   ||||||      |     |  ||  || |      || ||||| | ||   | | || | | ||  |||||   |  | ||  |||| |||||||||| || || |||||| | |||||||||||||| |||||||||||||| |  ||||| || || ||||| || || ||||| |||||||| ||||
--tgggccggtctctttaataaa---tagagagtaacattttgtttaccgttgagtgacatatttgtcttacagtacttattcttttatttgtgttacatttcagGTTCTTCTAAGCCGGTTGAGGCTTTTCTTGAGTCCTGGATATCCATATGAAGAGACCTTGAGTACATTCCACAACCAAACTAGCATTATCATGTGTTCCT

upper sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------tctttgatgttcctattaat--atcatccatgatcttgcaggttatggtaattttagtgaaaatacatttgactgatttgatctttgtcatcttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT
                    ||    ||||  | ||  |     || |||| ||||   | | ||  |    |||   | | |||  ||||||  |||||      |  |   |  ||||| | ||  |||| || |||||||||||  |||||||||| |||||||||||||||||| | |||||||| ||||||||||| |||||| |||||||||| |
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatg-tcttcttgatcat--ttgccttaaccatactactcttgactcttttgaatccctt--ttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT

upper sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
tctttgatgttcctattaatatcatccatgatcttgcaggttatggt---aattttagtgaaaatacatttgactgatttgatctttgtcatcttgt-atttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT
  ||  |||||  |   ||||  ||      | |||   |  |  ||   ||  | |  |    | ||||   ||||| || | | |||  | || | | |||||| || || || |||||||| ||||||||||| |||||||||||||||||||||||| ||||||| ||||||||||| || |||||||| |||||||| |
-tttgcatgttgat-caaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcatt--gctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT

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|4296298|gb|AI442455.1|AI442455
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|37994320|gb|CF806066.1|CF806066
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|16106049|gb|BI893789.1|BI893789
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|7478635|gb|AW666343.1|AW666343
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|26048689|gb|CA785142.1|CA785142
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|5605872|gb|AI899970.1|AI899970
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|14990101|gb|BI315774.1|BI315774
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|7588237|gb|AW704037.1|AW704037
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|33389935|gb|CA853142.1|CA853142
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|6454405|gb|AW185088.1|AW185088
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|21888159|gb|BQ741372.1|BQ741372
EST:     GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GCCCTGATTATGGGGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
EST: gi|21637832|gb|BM107987.1|BM107987
EST:     GATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA
genomic: GATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaattttagtgaaaatacatttgactgatttgatctttgtcatcttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT
                                        tcatctt  CT-rich tract
            aaaatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgatgttcctattaatatcatccatgatcttgcaggttatggtaattttagtgaaaatacatttgactgatttgatctttgtcatcttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT

- - tgatgtt
- - - - - - - - - - -tcatcca
- - - - - - - - - - - - - - - - - tgcaggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg