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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag

Basic information

species Zea mays
transcript GRMZM2G094255_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g52710.2 (Oryza sativa), 5'ss of exon 6
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag
|| ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| |                                                                   
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccag------------------------------------------------------------------

upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g52710.3 (Oryza sativa), 5'ss of exon 6
-------------------------------------CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaag
                                     || ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| | ||     |||||  |   | |    |||   |   |||||| |  ||    |  |   |||| |||||
CTTAGACAGCTATTGATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagtta----agcgagctaagaag--tacgtatatcatacctgagcctgccttttctttgctcttatgaag

upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 6
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaag
|| ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| | ||     |||||  |   | |    |||   |   |||||| |  ||    |  |   |||| |||||
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagtta----agcgagctaagaag--tacgtatatcatacctgagcctgccttttctttgctcttatgaag

upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G28420.2 (Glycine max), 5'ss of exon 6
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag
 |||| ||||| |||||||||||  |||||||||| ||||| ||||| |||||||| |  ||||||   ||   |      ||| |   | || |  |||       |  ||  || | | |  || |  ||      | |   |||| |||| ||| || |||   ||                                                                                              
TTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatacatagaacttcataatcagttatagtca------ttaaatttgtaa-atatattcatgcatatcattatgaaagaaacatactgaatg-ctgtagatgt--------------------------------------------------------------------------------------------

upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G14910.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaaca-gctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag
 |||| || ||||||||||| ||  ||||||| || ||||| ||||||||||||||||| ||||||                  | || |||  | || ||| ||  |  |  || | | | ||  ||| |        |||  |       | |||||   |    | | |    |||||  |||| |  | ||||||| ||||  |                                                        
TTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAGgtat-------------taggattccaatctttcttaaagcatacgaggacaataacagaacgttaat-------gtttcatc------tgttgacaaacctttcttga---taagat--ttgattcatttctatttattatgacag------------------------------------------------------

upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT3G22425.1 (Arabidopsis thaliana), 5'ss of exon 5
-------------------------------------CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag
                                      |||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||||||||| ||||||| |  || |           ||||||  |||  ||   | |   ||||    | || |||    || | |  | || ||        |   ||| ||| | |  |   ||  |  |||   |  | | | ||| ||| | |                                                        
AGTGTTGCCAAAAATTGTTTAACCTTTCGATTTGTAGTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgat-----------tcaaatcttccaaaagctaacaaaatca----tgcagttt----catgagtttcttcta--------tcctctgtctgtggaccatttcataacagtt--ttaatatttgtttgttacaacag------------------------------------------------------

upper sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT3G22425.2 (Arabidopsis thaliana), 5'ss of exon 6
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag
 |||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||||||||| ||||||| |  || |           ||||||  |||  ||   | |   ||||    | || |||    || | |  | || ||        |   ||| ||| | |  |   ||  |  |||   |  | | | ||| ||| | |                                                        
TTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgat-----------tcaaatcttccaaaagctaacaaaatca----tgcagttt----catgagtttcttcta--------tcctctgtctgtggaccatttcataacagtt--ttaatatttgtttgttacaacag------------------------------------------------------

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|76010862|gb|DT938032.1|DT938032
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|31355338|gb|CD439695.1|CD439695
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|12970168|gb|BG266848.1|BG266848
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACCCCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|76284483|gb|DV024051.1|DV024051
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|94478728|gb|EB707686.1|EB707686
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|78107718|gb|DV526136.1|DV526136
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATTCGAGGCATCTTTTCAA-GCGT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCAT-CGAGGCATCTTT-CAAAGCGT
EST: gi|71327961|gb|DR800622.1|DR800622
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|60349510|gb|DN216483.1|DN216483
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|76289085|gb|DV028653.1|DV028653
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTTCAA-GCGTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTT-CAAAGCGTT
EST: gi|76010863|gb|DT938033.1|DT938033
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACATCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|74232835|gb|DT640749.1|DT640749
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|76293135|gb|DV032703.1|DV032703
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTTCAA-GCGTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTT-CAAAGCGTT
EST: gi|74232836|gb|DT640750.1|DT640750
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|76284484|gb|DV024052.1|DV024052
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAA-CTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|31664107|gb|CD573287.1|CD573287
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|78107717|gb|DV526135.1|DV526135
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
EST: gi|78112492|gb|DV530886.1|DV530886
EST:     TCTTCCAATCTGTGGGGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGGAAAACTCACCCCATATCATCGAGGCATCTTTCAAAGCTGTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGC-GTT
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG                         CTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT
genomic: TCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTT

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: 81

CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 47

CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 41

CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 50

CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattg ... tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCA