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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttacttgtgcaaaatcaactaaatgttagattagtttgtatcttcatcagcctttataaaggaaaaaattcaagtttttcaacaatctta...

Basic information

species Glycine max
transcript GLYMA04G41210.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41210.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os10g35810.1 (Oryza sativa), 5'ss of exon 2
TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttac-ttgtgcaaa--atcaactaaatgttagattagtttgtatcttcatcagccttt------ataaaggaaa----aaattcaagtttttcaacaatctta--
|| ||  |||| ||  | ||||| ||| | ||||||||||| || || ||| | |||||||| ||||| || ||||||||||| || || |||||||| |||||    | | || || ||  |   ||||    | || |  |||| |||  |   ||||   |||||      |||||   ||    | || |   | | ||||   | ||   
TCTCTAGCTGCAGCCTTGATGTCCGATTCAAAGTTTGATGGGGCCGACATGTCTGAAGTTGTGATGTCCAAAGCTTATGCTGTGGGGGCAAGCTTCAAAGgtaaactaactcaccttctgtcattcatcacactattgctgcatta-tttccaaaatcatgtacctttgaattgataaacagaacactagatgcttatatctcaattgttttcag

upper sequence: GLYMA04G41210.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G436710_T01 (Zea mays), 5'ss of exon 2
TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaa-----tatttacttgt-----gcaaaatcaactaaatgttagattagtttgtatcttcatcagcctttataaaggaaaaaattcaagtttttcaacaatctta--------------------------------------------------------------------
||  |  |||| || || ||||| || || ||||| || || ||||| ||| | |||||||| ||||| || ||||||||||||||||| || ||||| |||| |||     | |  || | |      ||| | |||| |  |     ||    |  | |  |  |   | |     | |      | ||  ||||   ||  ||  ||                                                                    
TCTTTAGCTGCAGCGCTGATGTCCGAGGCAAAGTTCGACGGCGCTGACATGTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaactaactgtgcacctctttttctcaagaacaaccatgtacagcatattctcctgttctggttcac-tgcgcgatgccgctgaatc--gtttactaaatataatactgcaatacagtaatactgaatagaacagaatgatgaggtccctctgggtcaaaatgctttatttcag

upper sequence: GLYMA04G41210.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G53490.3 (Arabidopsis thaliana), 5'ss of exon 3
TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttacttgtgcaaaatcaactaaatgttagattagtttgtatcttcatcagcctttataaaggaaaaaattcaagtttttcaacaatctta
 | || ||||| ||  | |||   |  || ||||||||||| || |||||||| |||||||| |||||||| ||||||||||| |  || ||||| || ||||   | | |||  | |  ||| |  |  ||   |  | | |  || |      |  |   || || || |    | |   | || ||    |      
ACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttgaaatttga--aagcatatggtaaaattatggaccaa--aatgttaattaatgttttagtgtgaattcttttctag-----

upper sequence: GLYMA04G41210.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0098g01540.t01 (Vitis vinifera), 5'ss of exon 3
TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttacttgt-gcaaaatc-aactaaat-gttagattagtttgta-tcttcatca-gcctttataaaggaaaaaattcaagtttttcaacaatctta
|| ||  | || |||||||||||||| || ||||||||||| || || ||| | || || || ||||||||||||||||| ||||| ||||||||||| |||||  |  || | || | ||    ||  ||||| | | | || || ||  || || ||||       |  |   ||||  | |   |||        |      
TCTCTTGCAGCAGCACTCATGTCAGAAGCTAAGTTTGATGGTGCAGACATGTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggttgattttttgccttctctgactaatttgcttgaatatttcatagtcctcatttcataatcttcttggaatgagtcttagtagacttgaag-----

upper sequence: GLYMA04G41210.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S319_46V6.1 (Physcomitrella patens), 5'ss of exon 3
TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttacttgtgcaaaatcaactaaatgttagatt--agtttgtatcttcatcagcctttataaaggaaaaaattcaagtttttcaacaatctta
 |  | || || || ||||||||||| ||||| || ||||| |||||  |||| |||||  | ||||| ||||| || || ||||| || ||||||||||||||   |   || ||  |  | | || | || ||  |  ||  ||  | |   ||  |||  ||      |      |  |||   | ||| | | |    
ACATTATCAGCCGCTCTCATGTCAGAAGCCAAATTCGATGGTGCTGACTTGACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaat--tcactatttcagtcataacagcaaagtgaaaagttccagcgtatggtttgttcattctcatgtcatcgttcatctcaccctattctatatttagt

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|7693207|gb|AW761303.1|AW761303
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAAG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|151403361|gb|EV273171.1|EV273171
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|298190185|gb|HO032306.1|HO032306
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|298169288|gb|HO020648.1|HO020648
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GAGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTG
EST: gi|298176429|gb|HO026664.1|HO026664
EST:     GACAGAAGTTGAAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTG
EST: gi|208207307|gb|GE007144.1|GE007144
EST:     GACAGAAGTTGTAATGCCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|23051927|gb|BU577116.1|BU577116
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|120531916|gb|EH260049.1|EH260049
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|26060058|gb|CA802972.1|CA802972
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
EST: gi|19348660|gb|BM893192.1|BM893192
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTG
EST: gi|12690636|gb|BG156972.1|BG156972
EST:     GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGG                         GGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG
genomic: GACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatat ... tattttacagGGGTGGACTTCTCAAATGCAGTCTTGGACCGTGTGAACTTTGAGAAAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttacttgtgcaaaatcaactaaatgttagattagtttgtatcttcatcagcctttataaaggaaaaaattcaagtttttcaacaatctta

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaaa