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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagccgtaaatatacaggacaacatttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta...

Basic information

species Glycine max
transcript GLYMA02G45880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45880.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g53490.1 (Oryza sativa), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagccgtaaatatacaggacaacat-ttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta--
| ||||||||||  |  | || || || |||||||||||||| || || || |||||||| ||||| || || || ||||| |||||||| || |||||||||  |  ||     |  ||   |  | | | | |  |  | || ||  | |  |  |   ||||  | || | | |   |  | | |  ||||  ||     
GAACTTTGACCCAATTCGCTACTCTGGTAGATGGTTCGAAGTAGCATCGCTGAAACGTGGCTTTGCTGGTCAGGGACAAGAGGACTGTCACTGTACTCAGgta--ttgtagtgccagaatcctcacacacaaatactagtagatcttaatctgtatgatgccccagca-atatgtacctctgaatcctgattcctgaaaacac

upper sequence: GLYMA02G45880.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G073743_T03 (Zea mays), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagccgtaaatatacaggacaacatttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta-----
  |||| || || ||  | || || || |||||||| || || || ||  | |||||||||||||| || || || |||||||||||||| || |||||||||     |  ||||  |  | |   ||| | |  ||| |  || |  | |||  | ||      |  |||           ||||||| |  ||   |      
AAACTTCGATCCAGTTCGCTACTCTGGTAGATGGTTTGAGGTAGCCTCGTTGAAACGTGGATTTGCTGGTCAGGGACAAGAAGACTGTCACTGTACTCAGgta----ttgtaatacctgaaacatcaaacacattggagaggatatc-tgtagccaggatttttctccattatctaaaaaagaacatctctgtctgtgtgatgat

upper sequence: GLYMA02G45880.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagccgtaaatatacaggacaacatttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta
| ||||||||||||| || || || ||||||||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||||| || |     || |    ||  |||| |     |  ||||    |    | |       |  |  |||   || || ||                 
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagt----ccacaaat-tgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag----------------

upper sequence: GLYMA02G45880.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv19s0177g00320.t01 (Vitis vinifera), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta-aaataaatatagccgtaaatatac--aggacaacatttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta
||| |||||||| || |||||||| ||||||||||| ||||| ||||| || |||||||||||||| ||||||||||||||||| || |||||||||||||||||||||    | |  |||    | |  |      ||||   |  |   |   |    ||   ||  | |   |  ||  |     |||| ||  ||||  
GGATTTTGACCCAGTGAGATATTCTGGAAGATGGTTTGAAGTAGCTTCCCTCAAACGTGGATTTGCTGGACAAGGCCAAGAAGATTGCCATTGCACTCAGgtaaatgctgtggacagttatgattggacctgagatgaggatttctatcctttggggcttgaatgcagaaaaagaaatctggtttctgatctctca-taat--

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|298176805|gb|HO023278.1|HO023278
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|193577920|gb|FK537014.1|FK537014
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|209702793|gb|BW652782.1|BW652782
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|51336360|gb|CO980226.1|CO980226
EST:     NTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACANNNGATAGGGAAGCACCATCNANCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|23053079|gb|BU577570.1|BU577570
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCTAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|298163009|gb|HO011742.1|HO011742
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTTATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|213617213|gb|DB971304.1|DB971304
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCNAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|209697285|gb|BW655500.1|BW655500
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|298164654|gb|HO014299.1|HO014299
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|298192899|gb|HO033333.1|HO033333
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCTAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|298174728|gb|HO014759.1|HO014759
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|298170097|gb|HO018721.1|HO018721
EST:     TTAAACGTGGATTTGCAGGACAAGGCCAAGAGGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gatatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagccgtaaatatacaggacaacatttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttccc