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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaaattttggatttttttttttttttttgctttccaaatggaaagggaataaatagatgtgtttgctgatgtgagtaattgttttattgctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA

Basic information

species Glycine max
transcript GLYMA16G13580.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G07110.1 (Arabidopsis thaliana), 3'ss of exon 3
ggaaaattttggatttttttttttttttttgcttt--ccaaatggaaagggaataaatagatgtgtttgctgatgtgagtaattgttttattgctaaca-cagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA
  | || | |    ||||    | | ||| | ||    ||  |   |     |  ||| |||   |  ||| |||  | |   ||||| ||    |  | |||||||| || || |||||||||||||  || |||   |||||||||||||||||||| || | |||| | || |  || |||||||||||||||||||| |
acataactgtactgttttaggatatctttagattggatcatgttttagttagaagaatggat-cataagctaatg--aatgtgtgtttgatgaaaatgagcagGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGAAAGAAGCAACTTAGCAAACTCAGAGCTAAGGCCGAGAAGGTTGCTGAAGAGA

upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G07110.2 (Arabidopsis thaliana), 3'ss of exon 3
---ggaaaattttggatttttttttttttttttgcttt--ccaaatggaaagggaataaatagatgtgtttgctgatgtgagtaattgttttattgctaaca-cagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA
     | || | |    ||||    | | ||| | ||    ||  |   |     |  ||| |||   |  ||| |||  | |   ||||| ||    |  | |||||||| || || |||||||||||||  || |||   |||||||||||||||||||| || | |||| | || |  || |||||||||||||||||||   
atcacataactgtactgttttaggatatctttagattggatcatgttttagttagaagaatggat-cataagctaatg--aatgtgtgtttgatgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGAAAGAAGCAACTTAGCAAACTCAGAGCTAAGGCCGAGAAGGTTGCTGAAG---

upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 3'ss of exon 3
ggaaaattttggatttttttttttttttttgctttccaaatggaaagggaataaatagatgtgtttgctgatgt-gagtaattgttt--tattgctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA
  | |||     || | | |  || ||  | ||    | | | |||  |      ||      ||| |||  || |  | | ||| |  |  |  |    |||||||| || |||||||||||||||| |||  | ||||  |||||||| ||||||||| | |||||| |||| || ||||| ||||||| ||| |  || |
-cacaatgc--aatctctataattcttaatactactgataagcaaactgtgggtttaatgacattttctgtggttgtctcactgtctcttgctattgttgcagGAGCTTGAGAAGAAGAGAAAGGAAAGGGCTGAGTTGGCCTATGAGAGGAAGAAGCAGTTGAACAAACTAAGAGTCAAAGCTGAGAAGGCTGCAGTGGATA

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|298178143|gb|HO027526.1|HO027526
EST:     TGGGCAGGTTGTCATCTGAGGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAG
EST: gi|193470062|gb|FK436843.1|FK436843
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAG
EST: gi|10846164|gb|BF071265.1|BF071265
EST:     GAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: GAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|298198649|gb|HO040188.1|HO040188
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACCATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAG
EST: gi|151411210|gb|EV281021.1|EV281021
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|192312241|gb|FK005698.1|FK005698
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|58018190|gb|CX704932.1|CX704932
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|298195471|gb|HO043862.1|HO043862
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACA
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACA
EST: gi|51334831|gb|CO978697.1|CO978697
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|58017414|gb|CX704156.1|CX704156
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|209717401|gb|BW684794.1|BW684794
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|17021875|gb|BM092909.1|BM092909
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAG
EST: gi|22932124|gb|BU549263.1|BU549263
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|18722168|gb|BM523389.1|BM523389
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|192312242|gb|FK005699.1|FK005699
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|298198972|gb|HO042335.1|HO042335
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGA
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGA
EST: gi|58017241|gb|CX703983.1|CX703983
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
EST: gi|14259082|gb|BG881990.1|BG881990
EST:     TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGG                         GAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG
genomic: TGGGCAGGTTGTCATCTGAAGTTGGATGGAGCTACTATGATACCATCAGGgtaagttctt ... gctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggaataaatagatgtgtttgctgatgtgagtaattgttttattgctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA
                                            tgctaac  putative branch site (score: 1)
                              agtaattgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaaattttggatttttttttttttttttgctttccaaatggaaagggaataaatagatgtgtttgctgatgtgagtaattgttttattgctaacacagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - - - - - - - -ggaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat