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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCATTCAGATGGATAACCTTACTGCTGACCCAGGAATTCAACTTCGCCGACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcgagcgcgcacactgtttcttctgctctggaattatctttggctctgtttctttgcctaaactttgtctgctgaacacag

Basic information

species Zea mays
transcript GRMZM2G068392_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 5'ss of exon 8
CGCATTCAGATGGATAACCTTACTGCTGACCCAGGAATTCAACTTCGCCGACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcgagcgcgcacactgtttcttctgctctggaattatctttggctctgtttctttgcct-aaactttgtctgctgaacacag
||||||| | ||||| ||  ||||| | |||||||| |||||||| || ||||| |||||||| ||||||||||||||||||||||||| ||| || |||||      | |     ||| ||| ||  ||    |  |  ||   |||   ||   ||| | |||| ||||||| ||||| ||   |||
CGCATTCCGGTGGATTACGCTACTGTTAACCCAGGAGTTCAACTTTGCTGACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaacaaa---acaccctggtttatcc-tgcaaggcttggtttt---tccagttcgtcgcctgaaactttatctgccgagtgcag

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G28660.1 (Glycine max), 5'ss of exon 8
CGCATTCAGATGGATAACCTTACTGCTGACCCAGGAATTCAACTTCGCCGACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcgagcgcgcacactgtttcttctgctctg---gaattatctttggctctgt--ttctttgcctaaactttgtctgctgaacacag-------
 ||||| || ||||| ||  | |||||||| ||||||||||| || ||||||| | ||||||| ||||| || || ||||| ||||| | ||| || |||||        |     || | |    ||| | || ||   || ||   ||| |   |||  | |  |||||    | |     |   | | ||       
TGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCGATCCAGATGGTCCACAGgtacaaatgtacaattcatatttaaccttgtactatgatcgacttgcatttagacttgtggtccactgcctcttgtataaaaacaatataaagctacttt

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA08G11760.1 (Glycine max), 5'ss of exon 8
CGCATTCAGATGGATAACCTTACTGCTGACCCAGGAATTCAACTTCGCCGACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcgagcgcgcacactgt-ttcttctgctctggaatt---atctttggctctgtttct-ttgcctaaa---ctttgt--ctgctgaacacag---
 ||||| || ||||| ||  | |||||||| ||||||||||| || || |||| | ||||||| |||||||| || ||||| ||||| | ||| || |||||      |        ||  |||  | |  |   | || |||   |  | |||| |  |  || |||  ||||   || | |  || ||  | ||     
TGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCTGACAGCCTTCACATTTGGGACACTCTTTTAAGCGATCCAGATGGTCCTCAGgtacaattcatattta-accttgtactataatcgacaggcatttaaacttatggcccactgcctcttgtataaaaaactatatagctacttgatactttta

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|28985507|gb|CB350674.1|CB350674
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|148935026|gb|EC879067.2|EC879067
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|18164380|gb|BM334219.1|BM334219
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|78076513|gb|DV504947.1|DV504947
EST:     ACACCATTCACATTTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|71309792|gb|DR791178.1|DR791178
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|71309794|gb|DR791179.1|DR791179
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|18171551|gb|BM341391.1|BM341391
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|211178282|gb|FL421437.1|FL421437
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCAC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|18170879|gb|BM340719.1|BM340719
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
EST: gi|60342736|gb|DN209709.1|DN209709
EST:     ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAG                         GAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC
genomic: ACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcg ... ctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCATTCAGATGGATAACCTTACTGCTGACCCAGGAATTCAACTTCGCCGACACCATTCACATCTGGGACACACTATTAAGTGATCCTGGTGGCCCCCAGgtgagccgcgagcgcgcacactgtttcttctgctctggaattatctttggctctgtttctttgcctaaactttgtctgctgaacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG