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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaaccctatcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG

Basic information

species Glycine max
transcript GLYMA20G38030.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 1
--------------gtatactct-tttctttctgtttcgtttttttccctgcttctgtaaccctaacc--ctatcgattacactatcttttttccttc-ttccgttttcttagccattag---ggtttctgattttaattgaattgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
              |    |||| | |||  |     | |   |  |||| | || |      |  ||   |  |   | |  |   | ||| | |   ||  | ||||   | | |  |   |||||  | ||||  |||   ||   || |||   | |||| ||| ||||| ||||||| |||||  ||||||||| |||||| ||||| |||||||| |||||||||||||||||||| |||||| | ||||||||||
gcaagcccgcctccgctctctctctctctcccctaaccctagatccccctccctccgaggtttttgccagttgcctcctccggtgaatctttgcttggattagggtttccgggtcgtctgatcggtttggggttttttttggtgtgattttggtg--cgcagGATGAGCTGCAGCGGACCAACTTGGAGCTGGAATCGTTCAAGGAGAAGATTAAGGAGAACCAGGAGAAGATTAAGCTCAACAAGCAGCTTCCCTACCTCG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 1
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaaccctatcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtcct-tcgtg-actgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                           ||| | ||   ||| |  | |   | |    |   || ||| |||||  ||        |  ||   |  ||| ||   ||||||||     |  |||||   ||| |  |   |||| ||| ||||| |||| ||  | ||  ||||||| |||||||| |||||||||||||| ||||||||||| || ||||| |||||| |||| ||||| |
--------------------------gtttgctctctctctctctctccgcctccgcgggaaaccctagcttttgccccagcgatctcctccatgggatttgg---tctgatttgtgggggtttgtctcatcgggtgcctcagGATGAGCTGCAGCGGACGAACCTTGAGGTGGAATCCTACAAGGAGAAGATCAAGGAGAACCAGGAGAAGATCAAACTCAACAAGCAGCTGCCTTACCTTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G032505_T01 (Zea mays), 3'ss of exon 1
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaacccta---tcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtgac-tgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                                      |  |  | || |  ||||    ||||  |      ||     ||||  |  |    || ||   | |   |   |  |||  |||  || ||  | |   |    |||| ||||||||| |||| ||  |||| ||||| |||| |||||| ||||| ||||| || || ||||| ||||||||||| |||||| ||||||||||||
-------------------------------------gtgagcgagcccagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttct-gatctgtggggtttgtttggtttttctcttgccgcacccagGACGAGTTGCAGCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAAGAGAAAATTAAGCTCAACAAGCAGCTGCCCTACCTCG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 1
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaacccta---tcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtgac-tgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG------------
                                      |  |  | || |  ||||    ||||  |      ||     ||||  |  |    || ||   | |   |   |  |||  |||  || ||  | |   |    |||| ||||||||| |||| ||  |||| ||||| |||| |||||| ||||| ||||| || || ||||| ||||||||||| |||||| ||||||||||||            
-------------------------------------gtgagcgagcccagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttct-gatctgtggggtttgtttggtttttctcttgccgcacccaggacgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAAGAGAAAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 1
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaaccctatcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                                     | | | ||||||| ||||| |     | ||     |   ||         | ||    |  ||  | ||   |||||    ||  |||  ||  |||     |||| ||| ||||| || | ||  ||||  |||| ||   |||||| |||| ||||||||| |||||||||||||||||||| |||||| |||| |||||||
------------------------------------gtgcggaaaccctagccctagc---cccgctgcgcgtcgcccag-----agtgtcgggactgttctgatt---gatttgggatgttttgggctgggtgttcatagGACGAGCTGCAGCGGTCGAACCTGGAGCTGGAGTCTATCAAGGAGAAGACCAAGGAGAACCAGGAGAAGATTAAGCTCAACAAGCAGCTGCCGTACCTCG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaaccctatcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                                    ||    | |   | |    || ||  |  ||| | | |||| |  | |   ||   ||    ||    || || || ||   |   |  |   | | || | | ||||||   ||| || || ||| | ||||  || || |||||||| ||||| ||||||||||||||||||||||| ||||| |||||| |||| ||| | |
------------------------------------ctcaactgagattgattgaattgaaaa-gcta-cgtctttcttgttgcaaattggata--tgttgaaattgctcatcttgtgtttttctttgatggggattta-gGAAGACGCGCAAAGAACAAATCTAGAATGTGATTCTTACAAGGAGAAGATTAAGGAGAATCAGGAGAAGATTAAACTCAACAAGCAGCTGCCTTACTTGG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 1
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaaccctatcgattacactatcttttttccttcttccgttttcttagccat--tagggtttctgattttaattga-----attgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                                                      | || ||| | || |||||||  |||  |   | |   |  || |  || | |||  |||||| ||  |      | ||  |  |    ||||||| |||||||||||||| ||  |||| | ||| || || ||||| |||||||||||||||||||||||||| |||||||| |||||| | |||||| | |
-----------------------------------------------------gtctctatt-ctctctctttttctctttatatatgtgtctttccgtgatatgatttgcgattttgatgaatggtggtggtggtatggtgttgaagGAGGAGTTGCAGAGGACGAACATGGAGTGGGACTCCTATAAGGAGAAGATCAAGGAGAATCAGGAGAAGATCAAGCTCAACAAGCAGCTTCCCTACTTGG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatactcttttctttctgtttcgt---ttttttccctgcttctgta---accctaaccctatcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtg-actgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
|| |  |||   | ||  || | |      |  | | || ||   ||   |   ||  |  |    || |        | |     | |  | ||   | |   |  |  ||    ||    || | || |       || | |  |||| ||   ||| ||        |||||   ||  |    || || || |||||||||||||| |||||||| ||||| ||||||||| |||| ||||| |
gttttttctgcgccttgagtatggcgcgcctggttcatggttggatatgtatgttagtctgaggtcttgctgggggggtgtagtagcatggggttgtgtcgaggtgtgaattatcaat---gatcggatgggtgggattggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATCAAGGAGAATCAAGAGAAGATCAAGCTGAATAAGCAGCTGCCTTACCTTG

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|6566718|gb|AW234350.1|AW234350
EST:     ACATCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|209727224|gb|BW663197.1|BW663197
EST:     ACATCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|192298921|gb|FG987666.1|FG987666
EST:     ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|192294338|gb|FG987267.1|FG987267
EST:     ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|192317513|gb|FK008965.1|FK008965
EST:     ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|209718510|gb|BW662655.1|BW662655
EST:     ACATCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|207838402|gb|GD811940.1|GD811940
EST:     ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATC
EST: gi|208096900|gb|GD894203.1|GD894203
EST:     ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAG                         GAAGAGTTGCA
genomic: ACATCGTCAGAGCTTCACGTCTTCTCGACAACGAGATTCGCATCCTCAAGgtatactctt ... gtgactgaagGAAGAGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttagccattagggtttctgattttaattgaattgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                         ttttaat  putative branch site (score: 3)
                                       tccttcgt  putative PPT
                      tgattttaattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactcttttctttctgtttcgtttttttccctgcttctgtaaccctaaccctatcgattacactatcttttttccttcttccgttttcttagccattagggtttctgattttaattgaattgtccttcgtgactgaagGAAGAGTTGCAGAGGACCAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA