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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGGGATTGCAAAGCTGGGGATTGGAAGAATAAGTGTTACCGCTGTGGGGAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtgctatatagtttccaaggtgctgctgcttttgtgttgtcttaacatggttatttcatttgaatggggtctctgagatctaaactgacgatgttaatctgtctggttcaagcaccag

Basic information

species Glycine max
transcript GLYMA19G35980.5
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35980.5 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 5'ss of exon 5
CACGGGATTGCAAAGCTGGGGATTGGAAGAATAAGTGTTACCGCTGTGGGGAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtgctatatagtttccaaggtgctgctgcttttgtg-ttgtcttaacatggttatttcatttgaatggggtctctgagatctaaactgacgatgttaatctgtctggttcaagcaccag
|| | || ||||| ||||| || |||||||| || ||||||||||||||||||||||| || |||||||| |||||  | |||||||| | |||  | ||||||    || ||  | | |   |    |  || ||  |||   ||||    |    | || |  ||||||||    |  || |||| |   |     ||  |  ||| | |  ||||        
CAAGAGACTGCAAGGCTGGTGACTGGAAGAACAAATGTTACCGCTGTGGGGAGAGAGGTCACATAGAAAGAAACTGTCAAAACAGCCCAAGAAATCTCAGgtattgattgataagttgatctgataaaga-gcagcacttgcaattgttccga----ggtactgtatttgaataatttaacttagatttctccaatgcatact--tctttttttttcag-------

upper sequence: GLYMA19G35980.5 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 5'ss of exon 3
CACGGGATTGCAAAGCTGGGGATTGGAAGAATAAGTGTTACCGCTGTGGGGAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgtt---gtgctatatagtttccaaggtgctgctgcttttgtgttgtcttaacatggttatttcatttgaatggggtctctgagatctaaactg--acgatgttaa---tctgtctggttcaagc-accag------------
| || |||||||||||||| || ||||||||||||||||| || ||||| || ||||| ||||| ||||| |||||| ||||||| ||||  ||  | ||||||  |    || |   ||  | ||||     | |   | |  || || ||| ||||  || ||||  |   ||    |   | ||    | ||||  ||  ||  ||   | |||  | || || | |  |             
CTCGAGATTGCAAAGCTGGAGACTGGAAGAATAAGTGTTATCGGTGTGGAGAAAGAGGTCATATTGAAAGAAACTGCCAGAACAGTCCCAGGAAGCTCAGgtattctcatatggtgattacatgccaaaacatttc---tctcctgctgccttgacat--ttttttccatattatatttttgttaagcatgatactgttactgtgcaaagtttttgttagcttaaaactattatgttatattgcag
















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|15286621|gb|BI470512.1|BI470512
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAAGTCACGTTCACCTCATCG
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
EST: gi|193427745|gb|FK394401.1|FK394401
EST:     AGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTAGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATC
genomic: AGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATT-GAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATC
EST: gi|208263419|gb|GE063329.1|GE063329
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|193479319|gb|FK445000.1|FK445000
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|151410994|gb|EV280809.1|EV280809
EST:     GGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGCACCAG                    
genomic: GGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATT--G----AGgtatgttgtg ... caagc
EST: gi|207788796|gb|GD761152.1|GD761152
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
EST: gi|193556594|gb|FK515247.1|FK515247
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAG                         C
genomic: GAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccag-
EST: gi|58015478|gb|CX702220.1|CX702220
EST:     AGCCCCAAAAAATTGAG                         GCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG
genomic: AGCCCCAAAAAATTGAGgtatgttgtg ... caagcaccagGCGAGGACGGAGTTATTCACGCTCACCAGTCAGGTCACGTTCACCTCATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACGGGATTGCAAAGCTGGGGATTGGAAGAATAAGTGTTACCGCTGTGGGGAGAGAGGACATATAGAAAGGAACTGCAAGAACAGCCCCAAAAAATTGAGgtatgttgtgctatatagtttccaaggtgctgctgcttttgtgttgtcttaacatggttatttcatttgaatggggtctctgagatctaaactgacgatgttaatctgtctggttcaagcaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC