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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgcatctatcctaaattcttatgtacagagcactatgctgcaaaggaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC

Basic information

species Glycine max
transcript GLYMA11G11960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 5
agtgcatc-tatcctaaattcttatgtacagagcactatgctgcaaag----gaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
 ||   |  ||  |  |||  || ||          |||  |    ||    ||| |   ||||||       | | ||   ||  || |||   | ||   |||||||||||||||||||||||||||||||| || || ||||  || |||||||||||  | ||||| |||||  | |||  ||| || |  | ||||   |
-gtttgtgatacacagaatctttgtgatgtagattttatttttttcagttttgaagttaagcatcaaaacttctgaagagctgaacttatttgtgtattggacagGTAGAAACAATTGATGACTATGATGAATACTGCCATTATGCTGCAGGACTTGTTGGTTTAGGTTTGTCAAAAATCTTCATTGCTTCGGAATTAGAAATAC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 5
-agtgcatctatccta--aattcttatgtacagagcactatgctgcaaaggaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
 | || ||  |   ||  ||  ||||| || | ||   | |   | || | |||   |   | | |  |||  |    |     ||||     || |   |||||||||||  |||||||||| |||||||| || |||||||| || || ||||||||  | ||||| || || || ||||  ||  | || ||||| | | 
aattgtattgaaagtaccaaaacttatttata-agttttgtaaagaaatgaaatcatttgtttacc--gatccagttgatccagttttcactattatacacagGTAGAAACTGTTGATGACTACGATGAATACTGCCACTATGTTGCTGGGCTTGTTGGTTTAGGTTTGTCGAAACTCTTCCTCGCTGCAGGATCAGAGGTTT

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 5
-agtgcatctatcctaaattc--ttatgtacagagcactatgctgcaaaggaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
 |  |||      ||||||||   | || |    || | |   | |  |  |||      ||    || |  | |||         || |  |  | || ||||| ||||| ||||||||||||||||||||||| |||||||| || |||||||||||  | || || || |||||||||||||| ||    |  |||||| 
aatagcactagaactaaattcatctttggattatgcccaaaagttctgaaaaata---aaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT

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|14010995|gb|BG725917.1|BG725917
EST:     ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG                         GTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTT
genomic: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAGgtttgtcgca ... ttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTT
EST: gi|208160470|gb|GD958766.1|GD958766
EST:     ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG                         GTAGAAACAATTGATGACTATGATGAATATTGTCACTAT
genomic: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAGgtttgtcgca ... ttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTAT
EST: gi|209722769|gb|BW682867.1|BW682867
EST:     ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG                         GTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGG
genomic: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAGgtttgtcgca ... ttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGG
EST: gi|20813646|gb|BQ298124.1|BQ298124
EST:     ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG                         GTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTT
genomic: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAGgtttgtcgca ... ttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTT
EST: gi|209725283|gb|BW672760.1|BW672760
EST:     ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG                         GTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCG
genomic: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAGgtttgtcgca ... ttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
                tcttgat  putative branch site (score: 4)
                                    tttttttatttttttc  putative PPT
                     atttatgacaagagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgcatctatcctaaattcttatgtacagagcactatgctgcaaaggaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC

- tgcatct
- - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - -tcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaag