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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctcgtgttttgtagattggtactttggctttcaactataaatgttaaatctaagttctctgacatgattagcctaataacagtaggagcctta...

Basic information

species Zea mays
transcript GRMZM2G007555_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 5'ss of exon 5
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctcgtgttttgtagattggtactttggctttcaactataaatgttaaatctaagttctctgacatgattagcctaa----taacagtaggagcctta
|||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| | |||||| ||||||||||| |||||||||||| ||    ||  ||||| | | || |||     ||| ||||  |  |  ||  || ||  | | |||  | | || |      ||   | |  ||     
TTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGAAGATTGACTgtgagttcagacgtactgtagctagatattttactcctcatctatgcagttctaaattatgtattgtcacaataatggcttggagcttatttgcaaaagt----

upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G44580.1 (Glycine max), 5'ss of exon 5
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctct----cgtgttttgta-gattggtactttggctttcaa-----ctataaatgttaaatctaagttct-ctgacatgattagcctaataacagtagg-agcctta------------------------------------------
|| ||||||||||| |||||||| ||  | || |||||||| ||||||||||||||||| || || ||||||||||| ||| ||||||| || || || |||  | | |      | |||| ||  |||  || ||| || | ||      || ||||| | | | | | |  |   ||| || |      ||||     | |  | ||||                                           
TTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATAAGATCGAATgtatgttgtacaatattttttctacaattattattttagcatacagattttctgtaaatttaataacaatgcacaattgaaatcaagtctttaattttctttgataacctttttaaataaacaaaaattgaacccatgtgatatcatgtttcag

upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 5
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctcgtgttttgtagattggtactttggctttcaactataaatgttaaatctaagttctctgacatgattagc-ctaataacagtaggagcctta-------------------------------------------------------------------------------------------------
|||||||| |||||||||||||| ||  | |  |||||||| ||||| ||||||||||| || |||||||| ||||| ||  ||||||| || ||||| ||| ||         | | ||||     ||||| ||| ||   | ||  ||||  ||||  ||| |   |   ||   ||  | ||   |   |||||   |                                                                                                 
TTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatgacaaatgtttaga---agactttagctatctggtctac-tgttttatctgggttttg-aatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcccaactcttcctttttgcag

upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 6
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagct-ctcgtgttttgta------gattggtactttggctttcaactataaatgttaaatctaagttctctgacatgattagcctaataacagtaggagcctta--------------------------------------------------------------
 | |||||||||||||||||||| ||  |||| |||||||| ||||||||||||||||| || |||||||| ||||| ||  ||||||| || || || |||  | | | |   |||| |        |||  || ||| || |  |  | |  || ||  || |      |     |  ||  ||  ||    | |     | |||                                                              
-TATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAAGATCGAATGtatgttgcacaaatttttttccctacaattattatttttgcatgaatttttctatattctatttttaaatttaagaacaat--gcacaactggaatcaagtctttaattttctttaataacatttttaaataaaccaaaattgactccatatgatatcatgtttcagt

upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 6
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgag-ctctcgtgttttgtagattggtactttggctt---tcaactataaatgttaaatctaagttctctgacatgattagcctaataacagtaggagcctta
|||||||| |||||||||||||||||  | || ||||| |||||||||||||||||||| || ||||| || ||||| ||  | ||||| |||||| |||||  | | ||  |   |||||  |    |    |  |    | |   || |||| || ||   | || | ||                                
TTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACAAAATTCACTgtacgtcccttttagcttgtatctcaaaaacaagattgggataacacattaatgatatatactatttttttgcag-----------------------------

upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 6
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctcgtgttttgtagattggtactttggctttcaactataaatgtta---aatctaagttctctg-acatgattagcctaataacagtaggagcctta------------------
||||||||||||||||| ||||||||  | || ||||| || ||||| ||||||||||| || |||||||| ||||||||| | || || || |||||||||  |   | |  | ||  | | | | |  |  |    || ||||| |  |||    || |       ||  |  | |       |||| || ||  ||                       
TTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACAAGATTGACTgtacgtctttg-atcttacaaagttg-atctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcag

upper sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 5'ss of exon 4
TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctcgtgttttgtagattggtactttggctttcaactataaatgttaaatctaagttctctgacatgattagcctaataacagtaggagcctta----------------------------------------------------------------------------------------------
||||||||||||||||||||||||||  |||  |||||||| ||||| ||||| ||||| || |||||||| ||||| ||| |||| || |||||||||||| || | | ||   |   ||      |      |||     | |   |||   |   |     |  || |     ||   |   ||| |  |     |                                                                                               
TTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACAAAATTGACTgtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcag

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|149111971|gb|EE191131.2|EE191131
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
EST: gi|149077489|gb|EE166185.2|EE166185
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
EST: gi|71319028|gb|DR796259.1|DR796259
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
EST: gi|148944608|gb|EC889738.2|EC889738
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAG

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), 49 (downstream exon)
Score: 146

TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 129

TTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGACTgtgagctctc ... attactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTACATTGAGAGACAAGAG