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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgtgatacttagggcatgtgcacagtttgtttgattccaaaataaggcatgtacataacggcagattatgttgatgtggtcaagatgaatagt...

Basic information

species Zea mays
transcript GRMZM2G112672_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 5'ss of exon 4
TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgtgatacttagggcatgtgcacagtttgtttgattccaaaataaggcatgtacataac--ggcagattatgttgatgtggtcaagatgaatagt------
|| || ||||||||||||||||| ||| | ||||| ||||||||||| || |||||||||||||||||||| ||||| ||  | || ||||| || || ||||||| |         |  |||| ||    | | | || | | |||||||  ||   |   | |   || ||  |||          |  | | | | |        
TTGTTCGATACAAAACACAATGGTATTTTAGGATTCGAAGAATTTGCCCGTGCGCTCTCAGTATTTCATCCAAATGCACCTCTCGACGAGAAAATTGACTgtaagtgta--------aatgcatctgggtgggtagcttaactacaaaatatagcgccttactgatagggaagtctataacctaaaaatagaaaaggacacatctatg

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G44580.1 (Glycine max), 5'ss of exon 5
TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtt-tgtgatacttagggcat-------------gtgcacagtttgtttg---attccaaaataaggcatgtacataacgg------cagattatgttgatg--tggtcaagatgaatagt-----------------------------
|||||||| ||||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||| ||||| ||| | ||||| |||||||| |||| ||| |   ||| ||     |              |   |||| || | ||   |||  | || || |||       ||          |  ||   |||||      |  | || || |                               
TTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATAAGATCGAATgtatgttgtacaatattttttctacaattattattttagcatacagattttctgtaaatttaataacaatgcacaattgaaatcaagtctttaattttctttgataacctttttaaataaacaaaaattgaacccatgtgatatcatgtttcag

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G00830.1 (Glycine max), 5'ss of exon 5
TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt--gatacttagggcatgtgcacagtttgtttgattccaaaataaggcatgtacataacggcagattatgttgatgtggtcaagatgaatagt-------------------------------------------------------------------------------------------
|| ||||||||||| ||||| ||||| ||||  |||||||| ||||| || || ||||| || |||||||||||||| ||  | ||||| ||||| |||||||||  ||    ||  ||||   |  |   |  | || |  | |     ||  ||  | |  |||     ||  | | |||  | ||   || |  ||  |                                                                                           
TTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAGTTTGCACGAGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatgacaaatgtttagaagactttagctatgtggtctacttttttatctgggttttgaataggaagagcatttattggagagg--gagctagatcatgttttgtttctgtagtttatttatttccttaatgcattagttattaatagtaatgcatatgttgggcatttccaacttttcttttttgcag

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 5
TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt--gatacttagggcatgtgcacagtttgtttgatt--ccaaaataaggcatgtacataacggcagattatgttgatgtggtcaagatgaatagt-----------------------------------------------------------------------------------------
|| ||||||||||| ||||||||||| ||||  |||||||| ||||| || || ||||| || |||||||||||||| ||  | ||||| ||||| |||||||||  ||    ||  ||||   |  |   |  | || |  | |     |  |  |   || |    | ||    ||||  | | | |  | |||| | |  |                                                                                         
TTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatgacaaatgtttagaagactttagctatctggtctactgttttatctgggttttgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcccaactcttcctttttgcag

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 6
TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtt-tgtgatacttagggcatgtgcacagtttgtttga-------ttccaaaataaggcatgtacataacggcagattatgttgatgtggtcaaga--tgaatagt---------------------------------------------------------
 ||||||| ||||| ||||||||||| || || |||||||| |||||||| || ||||| || |||||||| ||||| ||  | ||||| |||||||| |||| |||     |   ||    | |      | | | ||||        || | | ||      | || ||    | | | |       ||   |||||   | |||  |                                                         
-TATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAAGATCGAATGtatgttgcacaaatttttttccctacaattattatttttgcatgaatttttctatattctatttttaaatttaagaacaatgcacaactggaatcaagtctttaattttctttaataacatttttaaataaaccaaaattgactccatatgatatcatgtttcagt

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 6
TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgtgatacttagggcatgtgcacagtttgtttgattccaaaataaggcatgtacataacggcagattatgttgatgtggtcaagatgaatagt
|| ||||||||||| |||||||| || || || ||||| ||||||||||| || ||||| || ||||| || ||||| ||  | ||||| || ||  | |||| ||        |||   || |||             ||||     ||||  ||  |  || |    | | ||| ||  ||  |              
TTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACAAAATTCACTgtacgtcc------cttttagcttgtatctcaaaaacaagatt--gggataa--cacattaatgata-tatactatttttttgcag--------------

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|5846848|gb|AI999931.1|AI999931
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211265415|gb|FL346370.1|FL346370
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|31360067|gb|CD444424.1|CD444424
EST:     CAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: CAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|60354409|gb|DN221382.1|DN221382
EST:     GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|6194508|gb|AW146612.1|AW146612
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|78021323|gb|DV489710.1|DV489710
EST:     TGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: TGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211071789|gb|FK958795.1|FK958795
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|9952360|gb|BE638943.1|BE638943
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211483288|gb|FL326631.1|FL326631
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGARAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211071790|gb|FK958796.1|FK958796
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG

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), 46 (downstream exon)
Score: 114

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 173

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG