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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgt-ccactgttcta-aaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                                                      ||| |||||| | |  | | |  ||||||  |  || |         |     ||||   |  ||  | |    ||| ||| || | ||||| ||||||| || ||| |||| || ||| ||||||| ||||| || || || || || |||||| |||||||||||||||| || |||||||| || 
-----------------------------------------------------gtgtgccactgctttgcatatgttatatgtgccgattaataaccgtgaagga-gtttattgtgacacgtta----aatgttccat-gcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaa-agaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                                        || |  |    ||   |||  ||| ||  |  ||  || |||||  ||      |||||| ||| || |         |||||     || || ||| | ||||||||||||| || ||  | || || ||  ||||||||||||| || || || || || |||||| |||| |||||||||||||| ||||| || || 
---------------------------------------gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgta-----taacagttatgatgt---------tttga-----atatttaat-gcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
     | | ||||     | | ||  |  ||    ||   |||    | |  ||||    ||||  ||    | | | || ||  | |||      ||||  | || | | || | ||  ||          |  ||| ||||||||||||| || ||||| |||||||| ||||||||||| || || || || ||| | || ||  |||||||||||||||| || ||||||||||||
-----gtacctatta---agttgtaaaggaaaaaaaaccataagttgaataggatgagt-ctgtgttat--tgtagtctgaaattgctga------caga-gtcatattctctttaat--ga----------ctgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaag---aaatatgtaacagt-tgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                            || |    || ||     |      ||   ||     || |||||   || | |||   | | |||| ||  |||| |  | ||      ||  || |   |      |  ||| ||||||||||||| || ||||| |||||||| ||||||||||| || ||  | || ||| |||| ||  |||||||||||||||| || ||||||||||||
---------------------------gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaa-agttgttaattctcttaaatga------ctgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                                              || ||     |    | |  |     | | || || | | ||   ||    | |||         || |  | |||||  |   || | ||  ||||||||||||| || ||||| ||||||||  ||||||||||||||||||| || ||||| || ||| |||| ||||| || ||||| || || ||||||
---------------------------------------------gtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataa--------ctattgtatgagatgaccattta-ttacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGGCCTGGACGAATTGACAGGAAGATTGAGTTCCCAAATCCCAACGAAGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------gtaaagg---agctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttg-aacttaacagatattatttaccctctcatttgagaaaa--attttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                                          ||    |   |  | || | || | ||||||| |   | ||| |       || || | |    | | |||  |  |       ||  |||| || ||    ||   | | |  | | || | ||| || |  ||    | ||  ||||||| ||||| || ||||| |||||||| || || ||||||||||| || ||||||||||| ||| |||| ||||| |||||||| || ||||  |||
gtactattaataattgctaccctttttgcttctgctgtagttgtgtgtgcccacttgtattatatttgtgtatttatatgtattatgt-----gtgtggtatttgttat-ctagtagaatcagcaaaatggttggaaattggtggaatctgtatgtcatatc-tgtgacaacatgatcaatattttcagGTTTTAATGGCTACAAATCGAATTGATATTCTTGACCAAGCCCTCCTCAGGCCAGGACGGATTGACAGGAAGATTGAGTTTCCAAATCCCAATGGGGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccac-tgttctaaaaagaaat---atgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                                     ||       ||     |    ||| |||||| ||||         |||  | | |  ||||   |   |||||  ||   ||   ||| ||       | |  || |||| |||||||| || ||||| |||||||| || |||||||| ||| |  |||| ||||| || |||||||||||||| || || || || |  ||||||
-------------------------------------ttgggtgagtaaataaacaatcacatgttctgaaaattgccttcgtgttgctggttgactttcaactgattatcaactacctatcttggga------ctta--tgcagGTGTTGATGGCTACGAATCGAATTGATATTCTAGATCAAGCTCTCTTGCGACCCGGACGAATTGACCGGAAAATTGAGTTCCCCAATCCAACCGAAGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttca----attgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
                    | |   |   |  | || |  | | ||   |    || |     |  | ||||      |  |  ||||||       | |   |||   ||  |     |   |     | |   || |   | ||| |      |||||||||||||||||| |||||||| ||||||||| |||||||||||||  |  | || ||||| || |||||||| || || || || || || | |||||||
gtttgctcttcacaactgacacaattgaggtcatttacttatttgtttgagttgtttgtggtaattctatgatccttcatacttgaaaaagggtctcatcaatcttgctatttgccagcttagctcgaattgttcgttaactcacattgttgtaacattgtagGTTTTGATGGCAACCAATCGAATTGATATCTTGGATCAAGCCCTTTTGCGTCCTGGACGAATTGACCGGAAGATCGAGTTCCCCAATCCAACTGAAGAG

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|214009603|gb|DB988312.1|DB988312
EST:     GATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: GATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|37995024|gb|CF806613.1|CF806613
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|192332825|gb|FK026826.1|FK026826
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|192332826|gb|FK026827.1|FK026827
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|17022699|gb|BM093733.1|BM093733
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|254318622|gb|GR832790.1|GR832790
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|193421449|gb|FK389622.1|FK389622
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|207714550|gb|GD696995.1|GD696995
EST:     TCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|15589715|gb|BI674331.1|BI674331
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|16284294|gb|BI946006.1|BI946006
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|16277739|gb|BI942538.1|BI942538
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|209727795|gb|BW658719.1|BW658719
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|16344411|gb|BI970006.1|BI970006
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|16344478|gb|BI970073.1|BI970073
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|254318623|gb|GR832791.1|GR832791
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATAT-CTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|7924399|gb|AW830425.1|AW830425
EST:     TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAG                         GTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
genomic: TGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGA
EST: gi|208125966|gb|GD925994.1|GD925994
EST:     ACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAAATAAAGAATACAAG                         GTTTTGATGGCC
genomic: ACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAA-TAA-GA-T-CAAGgtaaaggagc ... tcaattgtagGTTTTGATGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
    acttaac  putative branch site (score: 3)
                                          ttttc  putative PPT
                              atttgagaaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA