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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattatctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

Basic information

species Glycine max
transcript GLYMA20G38860.1
intron # 48
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 48
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 12
gtaag-tattatctatt-tatctttgtattcttcctggca--tgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
||||| |  ||   ||| |||   ||| ||  ||   | |  | | |    | |    |||||     || |     || | | ||||| || || ||||||||||| ||||| ||||||||  | ||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||||
gtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcagGGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGGTATTGGGGTTAAGGGAGAAGAAAGTTGGGAAGCCTGGTGGGATGAAGAA

upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 48
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
--------gtaagtattatctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
          ||| |||   | | ||||| |||| | |   |   |  | |||| | | |   |   ||||   | |    |  | ||||| | || || ||||||||||| ||||||||||||||  | || |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||
gtaagcagccaagcatt--ttgtgtatctatgtactataagttcaaattgtcatta-tgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 48
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 45
gtaagtattatctatttatctttgt-attcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
||||||  |      |||| | | | ||  |   ||    ||  | ||  ||    | |    |  | |   |    ||| || || ||||| || |||| ||| ||||||||||||||  | ||| |||||||||||||||| || ||||  |||||||||||||| |||||||||||||||
gtaagtggtgctatcttatttatatcatgttgagtgttgagtaacgtgtttctcattgaacaacaataaaattatgctttcagAGTCGTGGAGGACTTCAAAGAATGGACAAATTGGCTCTTTTACAGAGGTGGAATTGGTGTGAAAGGAGCTGAAAGCTGGGAAGCATGGTGGGAAGAAGAA

upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 48
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
gtaagtattatctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
|||||||| || | | ||  ||| | |   || |||  |  ||||||  | || |    |||  || ||    |  |||||||   ||||| || ||  | ||||||||||| |||||  | ||| ||||||||||||| |||||||||| |||||||||||| ||||||||||| ||||||
gtaagtatcatttttctaattttctctc--tcatggatttgctcatgttttattaaccatttgttttac----cccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA

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|208140913|gb|GD935255.1|GD935255
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGG
EST: gi|193376576|gb|FK343165.1|FK343165
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGACTACTCTACCGAGGTG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGG-CTACTCTACCGAGGTG
EST: gi|193717024|gb|FK649892.1|FK649892
EST:     TTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|193556241|gb|FK511464.1|FK511464
EST:     TATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|193471075|gb|FK436974.1|FK436974
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|254331761|gb|GR843611.1|GR843611
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|298188356|gb|HO035049.1|HO035049
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|208089199|gb|GD888252.1|GD888252
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATT
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATT
EST: gi|193524673|gb|FK482292.1|FK482292
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGG
EST: gi|208259567|gb|GE058421.1|GE058421
EST:     TGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|193448333|gb|FK415914.1|FK415914
EST:     TTTATTCAACCCATCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|19937309|gb|BQ081239.1|BQ081239
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta ... gcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
                                            tgctttttt  CT-rich tract
                        atgattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattatctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG