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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcctgaatatatgtgaatttctttcattggatgatgctatcttattctcaaggttgcttctggtatatttttttcataattgtgtatttctgttattgtatcttgttagcatttttacaaattccttttttgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG

Basic information

species Glycine max
transcript GLYMA09G39150.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgttcctgaatatatgtgaatttctttcattggatgatgctatcttattctcaaggttgcttctggtatatttttttcataattgtgtatttctgttattgtatcttgttagcatttttacaaattccttttttgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG
                                                          ||| | ||| | ||  | |||  || ||| |   ||| | | ||||   |  |     ||  | ||  |   ||||  | |  | |||| | || || |||||||| |||||||| || ||| | |  |||||| ||||||||| ||||||| | ||||| ||||||||||||
----------------------------------------------------------gtttcgtcttg-atcatatttatatcattttagttttttataattg---ccaggggatatcatcactgagaactttaatat-atgcagCTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAG

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 2
gtttgttcctgaatatatgtgaatttctttcat----tggatgatgctatcttattctcaaggttgcttctggtatatttttttcataattgtgtatttctgttattgtatcttgttagcatttttacaaattccttttttgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG
||||||      || | | |  |||||| |       ||||||||   | |  | | ||| |  | ||||  | ||| ||| ||     || || |  |||  | |  | || |                ||  || ||||    ||||||||||||||||||||||| ||||  || || ||| | |  |||||| ||||||||| |||||| |||||||| ||||||||||||
gtttgtcttcttatttctattgatttctcttgaagtatggatgattacaccagactatca-gacttcttcatgcatagtttatttg---ttctg-acctctactgtc-tgtcct----------------atctctctttt----ttcagCCACTTCCATTTTGTTCATGAGTGCGTTACTATATTAATGGACTCTGCAATTTTGTTCTTTGGAGTATTGCCTTGGTTTTGGAAG
















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|193418788|gb|FK384426.1|FK384426
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|15202361|gb|BI425361.1|BI425361
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|192302658|gb|FG994896.1|FG994896
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTAACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|193425164|gb|FK389893.1|FK389893
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTCGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|4396612|gb|AI495609.1|AI495609
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|209708354|gb|BW683944.1|BW683944
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|209723765|gb|BW657734.1|BW657734
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|213594940|gb|DB971799.1|DB971799
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT
EST: gi|193346112|gb|FK310528.1|FK310528
EST:     ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAG                         CCACTTCCATTTTGTTCACGAGTTCGTGACAATAGTGACAGACTCTACAAT
genomic: ATCAGCCAAGAGAAATTTGAGAAATCTAGAGCCTATAGTCTTGATAAAAGgtttgttcct ... tgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctgttattgtatcttgttagcatttttacaaattccttttttgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG
                                    ttccttttttgttgtt  CT-rich tract
                         atttttacaaattcct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcctgaatatatgtgaatttctttcattggatgatgctatcttattctcaaggttgcttctggtatatttttttcataattgtgtatttctgttattgtatcttgttagcatttttacaaattccttttttgttgttcagCCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG