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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgtaatacgtcatgtgctttatggagctctataatataccatctaatctttttcactgacctactgtgcagtcggaacatcaagctttccctt...

Basic information

species Zea mays
transcript GRMZM2G081848_T05
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081848_T05 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g07310.2 (Oryza sativa), 5'ss of exon 3
--------------------------------ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgtaatacgtcatgtgctttatggagctctataat-ataccatcta-atctttttca-ctgacctactgtgcagtcggaacatcaagctttccctt-----------------------------
                                |||||||||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| | |||||| |||||| ||||||  || |  ||||| ||    | |  || |  | |  ||   |   | |||||   ||  |   | |||    ||                             
ATGCTAAAATGCTGAATGCTCTTTGTTTTCAGATGACAAAGCTGGCAATTATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcag

upper sequence: GRMZM2G081848_T05 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g07310.1 (Oryza sativa), 5'ss of exon 4
ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgtaatacgtcatgtgctttatggagctctataat-ataccatcta-atctttttca-ctgacctactgtgcagtcggaacatcaagctttccctt-----------------------------
|||||||||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| | |||||| |||||| ||||||  || |  ||||| ||    | |  || |  | |  ||   |   | |||||   ||  |   | |||    ||                             
ATGACAAAGCTGGCAATTATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcag

upper sequence: GRMZM2G081848_T05 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 5'ss of exon 5
ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgtaatacgtcatgtgctttatggagctctataatataccatctaatctttttcactgacctactgtgcagtcggaacat--caagctttccctt------
|||||||||||||| || ||||||||||||||  |  |||||||||||||||||||||||||||| |||||  | |  |    ||    |  ||||||    |   | ||||  |   |   | ||| ||     |||||     ||   ||| |  |  ||  |  |||      
ATGACAAAGCTGGCAATCATTCCCTGTACTGTACTCTTGGAGACCCTTTTCTTCAGGAAGAAATTCAGgttaatgttgagactgt----ttttttatgacagtgc-tgatatgtcga-tgggcatttgcat--gtctacttgattgttataacctggcctgcagtgtctttaactt

upper sequence: GRMZM2G081848_T05 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 5'ss of exon 5
ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgta-atacgtcatgtgctttatggagctctataata-taccatctaatctttttcactgacctactgtgcagtcgga---acatcaagctttccctt
|||||||| ||||| || || |||||||||||| | ||||| ||||||||||| ||||||| ||| ||||   ||  ||   ||  | |    ||||   ||||  ||  |  |  | | |  |||| ||||  ||  ||   |  | |   |   | |   |  |   |   
ATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAGgtaaattcttacgcactcccttacttttacttagcttcatgctgctttcctatgttcttcttca--gatataaaatagaatttcatccatactgaaataaac---

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|89251400|gb|DY623186.1|DY623186
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCCAGCTTTCCC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCC
EST: gi|148967838|gb|EE019130.2|EE019130
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|148960883|gb|EE011564.2|EE011564
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|148997312|gb|EE035807.2|EE035807
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|50322320|gb|CO517446.1|CO517446
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|149110398|gb|EE190395.2|EE190395
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|31358400|gb|CD442757.1|CD442757
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|71328578|gb|DR800947.1|DR800947
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|148936002|gb|EC880058.2|EC880058
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAA-TTTAG                         TCGGAACATCAAAGCTT-CC-TTAGTGTGCTCCTTCTTGGGTGT-GGTGTT
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAA-GCTTTCCCTTAGTGTGCTCCTTCTTGG-TGTTGGTGTT
EST: gi|149102837|gb|EE288179.2|EE288179
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGGTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|149105555|gb|EE291088.2|EE291088
EST:     TTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAAGAA-TTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGGTTGGTGT-
genomic: TTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAA-GAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTG-TTGGTGTT
EST: gi|87152152|gb|DY396941.1|DY396941
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCT
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCT
EST: gi|148995261|gb|EE034502.2|EE034502
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGC
EST: gi|149097659|gb|EE183556.2|EE183556
EST:     ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG                         TCGGAACATCAAGCTTTCCCTTAGT
genomic: ATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgt ... tactgtgcagTCGGAACATCAAGCTTTCCCTTAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAGgtttgtttgtaatacgtcatgtgctttatggagctctataatataccatctaatctttttcactgacctactgtgcagtcggaacatcaagctttccctt

- - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA