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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgctctgaagtcattacactaattgattcttcatagctgctgcacttatcacatttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA

Basic information

species Glycine max
transcript GLYMA07G32850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00650.t01 (Vitis vinifera), 3'ss of exon 5
-tgttgctctgaagtcattacactaattgattcttcatagctgctg-cacttatcacattt-ctggta-ttgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA
 ||    |||     |||  | ||  ||  || ||  |  |||  | || | |  |  ||  || ||  |||| ||    |   |  |    ||   |  ||||||| ||| ||  || ||||| |||||||||||   ||| || |||||||||||||| |||||||||||||||||||| || |  || |||||||| || |
gtgagattcttgctacatc-ccctttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatagGATGCTCAGAATGATAACAGTCCCTACCTTGGCAGCATCTATACTTCATTTCAAGAAAGGGCAACCTTCATATCCCATGGCAGTACTGCCAGGCTCGCCA

upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 3'ss of exon 2
-------tgttgctctgaagtcattacactaattgattcttc-atagctgct-gcacttatcac-atttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA
       | |||||      |  ||    |  ||  || |||  |||    |  || |  |||| | |||| | | | |  ||  |   ||       ||   |  ||||||| ||| ||  || ||||| ||||||||||| | ||| || |||||||||||||| |||||||||||||||||||| || |  || |||||||| || |
gtgagattcttgctacatgctttttttttttttttttttttctgtagtcaatcacaatcttcactagttcttgaactcaagttcttcttctc-----catcttttcatagGATGCTCAGAATGATAACAGTCCCTACCTTGGCTGCATCTATACTTCATTTCAAGAAAGGGCAACCTTCATATCCCATGGCAGTACTGCCAGGCTCGCCA

upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00740.t01 (Vitis vinifera), 3'ss of exon 3
tgttgctctga--agtcattacactaattgattcttcatag---ctgctgcacttatcac-atttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA
 | |  | | |  |||   |  | || | | || ||  ||    | |   || |  |||| | |||| | | | |  ||  ||  ||       ||   |  |||||||   | ||  || ||||  || |||||    ||||| || |||||||||||||| |||||||| ||||||||||| || || || |||||||| || |
-gatattttcactagtttctttagtactcggttttttctaaagtcagtcacaatcttcactagttcttgaactcaagttctttttctc-----catcttttcatagGATGTGCAGATGGAAAACAATCCGTACCTATTATTCATCTATACTTCATTTCAAGAAAGGGCAACTTTCATATCCCATGGCAATACTGCCAGGCTCGCCA

upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00730.t01 (Vitis vinifera), 3'ss of exon 2
tgttgctctga--agtcattacactaattgattcttcatag---ctgctgcacttatcac-atttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA
 | |  | | |  |||   |  | || | | || ||  ||    | |   || |  |||| | |||| | | | |  ||  ||  ||       ||   |  |||||||   | ||| || ||||  || ||||||   ||||| || |||||||||||||| |||||||||||||||||||| || || || |||||||| || |
-gatattttcactagtttctttagtactcggttttttctaaagtcagtcacaatcttcactagttcttgaactcaagttctttttctc-----catcttttcatagGATTTCCAGACGGAAAACAATCCGTACCTTTTATTCATCTATACTTCATTTCAAGAAAGGGCAACCTTCATATCCCATGGCAATACTGCCAGGCTCGCCA

upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00550.t01 (Vitis vinifera), 3'ss of exon 1
-------tgttgctctgaagtcattacactaattgattcttcatagctgctgcacttatcac-atttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA
       | |||||       | ||    |  ||  ||||  |   | |   || |  |||| | |||| | | | |  ||  |   ||       ||   |  |||||||   | ||  || ||||  || ||||||   ||||| || |||||||||||||| |||||||||||||||||||| || || || |||||||| || |
gtgagattcttgctacatgcccttttttttttttttttctgta-gtcagtcacaatcttcactagttcttgaactcaagttcttcttctc-----catcttttcatagGATGTGCAGATGGAAAACAATCCGTACCTTTTATTCATCTATACTTCATTTCAAGAAAGGGCAACCTTCATATCCCATGGCAATACTGCCAGGCTCGCCA

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|15589782|gb|BI674398.1|BI674398
EST:     ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGCTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|15202727|gb|BI425553.1|BI425553
EST:     ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|22523220|gb|BU082031.1|BU082031
EST:     ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|8283038|gb|BE020599.1|BE020599
EST:     ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGTGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATATACACT
genomic: ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACT
EST: gi|15284868|gb|BI468759.1|BI468759
EST:     ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|7147165|gb|AW509087.1|AW509087
EST:     ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|14259346|gb|BG882246.1|BG882246
EST:     GACAATTCAGTACCTTATTGGGTCTGGGATG                         GATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: GACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcct ... tgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttatcacatttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA
                                     attgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgctctgaagtcattacactaattgattcttcatagctgctgcacttatcacatttctggtattgacctttcttgactgattgaaattgatggatagGATCCTCGGACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTTCAAGAGAGGGCAACCTTCATATCCCACGGAAACACGGCCAGGCTTGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
tgttgct
- - - - - - - - - - - - - - - - - - tagctgc
- - - - - - - - - - - - - - - - - - - - - -tgcactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg