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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc...

Basic information

species Zea mays
transcript GRMZM2G090747_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 5'ss of exon 3
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttc--ctgttttct-tgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc--
|| |||||||||||||||||||||||||| |||||||| ||||||||||| || |||||||||||||| || || |||||||| ||||| |||||||| ||||||||||||||    | || | |||||   || | |||| | || ||  | |||     ||||||   || |  ||   |  |   | |  | | |||  |  
AAATTTTTGAGGCAGCCTCATTTTATTGTATGGGATAATAGTGATCTCATTACACATGAAGTCATGGGAGGTTTGAAAAATGTGTATGCCATTGGTGCCGgtaatttctatttcctctcttgattgtttttgctatcttctgtaatcacggtagag-----catatactgttgtgatatttagcatggggtatgttggaatgcac

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01380.1 (Glycine max), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgtttt-cttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc
|| |||||||||||||| || ||||| |||||||||||  |||| ||  | ||||||||||| |||||||| ||||| ||||| ||||||||||| || |||||   ||| ||    |  | ||  | |   |     |||  |   |    | || |||||| |   || | ||   || ||||    | | |       
AAATTTTTGAGGCAGCCCCACTTTATAGTGTGGGATAATGGTGACCTTGTTACTCATGAAGTTATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaaaaactagtttatgtggttacattgtagagaacaacttagtagaagcaaataggtacatacagttttttttttcaaaaaaaatttagagtttagtgt-

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G31730.1 (Glycine max), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaattt-ctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc----
||||||||| | || || || |||||||| |||||||||||||||||| |||||||||| |||||||||||||| |||||||||||||| ||||| ||||||||  | ||| ||   | ||  |   || | ||   | |  |     |     ||  |   ||||||| || ||  |  |      |||   |  |   |    
AAGTTTTTGCGCCAACCACACTTTATTGTCTGGGATAACAGTGATCTCGTCACTCATGAGGTCATGGGTGGCTTGAAAAATGTCTATGCAATTGGAGCTGgtaagctactaattaattgttatatctttacatgccatgtcaaacttgc-----agtaatccatatcatcatgttttggtttgtgtaatgttgtctatttcactt

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G15900.1 (Glycine max), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgat-tacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc
|||||| |  | || || ||||||||||| ||||| |||||||| ||  |||| |||||  ||||||||||| | |||||||||||||| |||||||| |||||  |  |  | |  ||  ||   |    | |     | || |  |      ||  |  | |||    || |     |||    |    | | |  || 
AAGTTTCTACGACAACCACATTTTATTGTCTGGGACAACAGTGACCTTGTCACCCATGAGATCATGGGTGGCCTGAAAAATGTCTATGCAATTGGTGCCGgtaagcttcaaat-tagttaacagcataagttttacagctaatgtgaaacttgtagtaatctgtattgccatgtcttttatatgttgtaatggttgtgact

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G20840.1 (Glycine max), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttct--atttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc
|||||||||||||| ||||| ||||| |||||||||||  |||||||  | ||||||||| |||||||||| ||||| ||||| ||||||||||| || ||||||||||  ||||  || || || || |     || |   || || |||  | ||   |   ||     ||  ||     |  | ||    |   | |  
AAGTTTTTGAGGCAACCTCACTTTATAGTGTGGGATAATGGTGATCTTGTTACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctccattttcctcttacattgctatacattgtaaagaata-acttcatagaagctagtaggcaaatgctattttaagcaggaaatacataatat-

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G33340.1 (Glycine max), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaa--tttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc
|||||| |  | || || ||||||||||| ||||| |||||||| ||  |||| ||||| |||||||||||||| |||||||||||||| |||||||| |||||  ||   ||| ||   |  |||    |       |    | ||   ||      |   |||  |  ||| ||    ||   |  ||||    ||    
AAGTTTCTACGACAACCACATTTTATTGTCTGGGACAACAGTGACCTTGTCACCCATGAGGTCATGGGTGGCTTGAAAAATGTCTATGCAATTGGTGCAGgtaagattctaattagttaatagcacaagctttacagctaagaagtaacttgttctaatctgtattgccatatcttttatatgttataatggttgcgatt--

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G28970.1 (Glycine max), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaa-tttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc-----
||||||||  | || || || |||||||| |||||||||||||| ||| |||| ||||| |||||||||||||| |||||||||||||| || || ||||||||  ||||| ||   | ||  |   || | ||    |  | | | ||| |     ||  ||||||||  | ||  |  |      |||   |  |   |     
AAGTTTTTACGACAACCACACTTTATTGTCTGGGATAACAGTGACCTCGTCACGCATGAGGTCATGGGTGGCTTGAAAAATGTCTATGCAATAGGAGCTGgtaagcttctaattaattgttataactttacatg----caaggtcaaacttgcag--taattatatcatcgtgttttggtttgtgtaatgttgtcaatttcactag

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G07690.1 (Arabidopsis thaliana), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaag--atgggctagaaacc
|||||| | |||||| ||||||| || || |||||||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||| |||||||| |||||  || |  ||||||      |  |     |  |  |||||  |   |  |  |||    |    |  || |    | |||    ||| |||||     
AAGTTTCTAAGGCAGTCTCATTTCATAGTCTGGGATAATAGTGACCTCATTACTCATGAAGTAATGGGTGGCTTGAAGAATGTTTATGCCATTGGTGCAGgtaagatc-aggtgtcttaaatggttatctgaataatagtgattcaa--agtaaattactggaactggtg-atcagaggtcaaagtttatgagctag-----

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc---
|||||||| || |||||||||||||| |||||||||||  |||| || || || |||||||| |||||||| ||||| |||| |||||| ||||| ||||||||      ||    |  |  | |    | ||     |  || ||||   | ||  | ||||     ||   || ||  ||     |    || | ||    
AAGTTTTTAAGACAGCCTCATTTTATAGTGTGGGATAATGGTGACCTTATAACCCATGAAGTTATGGGTGGTTTAAAGAATGCCTATGCCATTGGAGCTGgtaagacagtttcccttagtgaattaggacttgggcattaaataacac---acagtgatatattattgtacgatatgataaatccctttatatatatacgtgt

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgattacactgg--agagctacatatatcattatattaagaataaaaagatgggctagaaacc--------------------------------------------------------------------------------------------------
|||||| ||||||| || ||||| || || ||||| |||||||| ||  ||||||||||||| |||||||||||||| ||||| ||||| ||||| || ||||| || | | | ||||| | |  ||    |  |     ||| |   ||     || | ||||||| |  ||  |    | | |||  |  || |  | |                                                                                                   
AAGTTTCTGAGGCAACCCCATTTCATCGTATGGGACAACAGTGACCTTGTCACTCATGAAGTTATGGGTGGCTTAAAGAATGTGTATGCCATTGGAGCCGgtaagttgt-tatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgattttccag

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ25021 (Selaginella moellendorffii), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc
   ||  |||||||||| |||||| | |||||||| ||||| || ||| | ||||||||||||||||| ||||| || || ||||| || |||||||| |||      || |  ||   |||   ||||| |||||    ||  ||    || |  | |  | ||| ||   |     | |                   
CGTTTCCTGAGGCAGCCGCATTTTGTGGTGTGGGACAACAGCGACCTCGTTACTCATGAAGTCATGGGAGGCTTGAAGAACGTCTACGCAATTGGTGCCGgt------tagtgttcaagttcttagtttcttgtttg---gaaaacgaaagaaatgttctaaaatctttggctcgctcacag------------------

upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ15326 (Selaginella moellendorffii), 5'ss of exon 2
AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttctatttgtctttttcactgtttcctgttttcttgattacactggagagctacatatatcattatattaagaataaaaagatgggctagaaacc
   ||  |||||||||| |||||| | |||||||| ||||| || ||| | ||||||||||||||||| ||||| || || ||||| || |||||||| |||      || |  ||   |||   ||||| |||||    ||  ||    || |  | |  | ||| ||   |     | |                   
CGTTTCCTGAGGCAGCCGCATTTTGTGGTGTGGGACAACAGCGACCTCGTTACTCATGAAGTCATGGGAGGCTTGAAGAACGTCTACGCAATTGGTGCCGgt------tagtcttcaagttcttagtttcttgtttg---gaaaacgaaagaaatgttctaaaatctttggttcgctcacag------------------

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|8516489|gb|BE123214.1|BE123214
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|148950390|gb|EC895955.2|EC895955
EST:     AAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: AAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|67026682|gb|CO455431.1|CO455431
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|5847455|gb|AW000534.1|AW000534
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|5525703|gb|AI861596.1|AI861596
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|149111430|gb|EE294933.2|EE294933
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|5268853|gb|AI770817.1|AI770817
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|6020445|gb|AW065373.1|AW065373
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|71320116|gb|DR796811.1|DR796811
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
EST: gi|6056476|gb|AW090866.1|AW090866
EST:     CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTG                         GTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT
genomic: CACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 169

AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 117

AAGTTTTTGAGGCAGCCTCATTTTATTGTGTGGGATAACAGTGATCTCATCACTCATGAAGTCATGGGTGGCTTAAAAAATGTCTATGCTATTGGTGCTGgtaatttcta ... tatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA