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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcgttgctgtcatgagtttctcagtttcatctgtcacaaaaactgttcttcagcgtgtagagttttatcactatgacttctgcattgttgatcaaagtttggcaatgccttcctgatttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGGGCATTGCTTACTGTCTTGAGCACATGCATCAGCTGCAAACACCAGCTGC

Basic information

species Zea mays
transcript GRMZM2G135359_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135359_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g18370.1 (Oryza sativa), 3'ss of exon 6
gtaagcgcgttgctgtcatgagtttctcagtttcatctgtcacaaaaactgttcttcagcgtgtagagttttatcactatgacttctgcattgttg-atcaaagtttggcaatgccttcctgatttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGGGCATTGCTTACTGTCTTGAGCACATGCATCAGCTGCAAACACCAGCTGC
                          |  | | || || |||| ||     ||| |  |         || | | ||| ||   | ||  |   || ||  || |||| |  ||   ||  | ||   | ||||| || ||||| |||||||| || |||||| | |||||||||||||||||||| || ||||||||||| ||||| |||||||||||  || |||| | || 
--------------------------tatgctgcacctatcaccaatttgattcatttg--------attctgttactctgtgctgtgggtcaatgtattgaaatttgactgtgttgtcacggttgtgctgcagTTAGAGAAGCCGAGAAGCTGGATTGGATGACGCGGCTCAGGATATCCATGGGAATCGCTTACTGTCTCGAGCATATGCATCAGCTTAAACCACCTGTTGT
















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|211161244|gb|FL160685.1|FL160685
EST:     GATGGTATTTGAATATGCTCCAAATGGGACACTTTTTGAGCATCTCCATG                         TCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
genomic: GATGGTATTTGAATATGCTCCAAATGGGACACTTTTTGAGCATCTCCATGgtaagcgcgt ... ttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
EST: gi|78117674|gb|DV536061.1|DV536061
EST:     TTTTTGAGCATCTCCATG                         TCAGGGAAGCAGAGAAGCTTGATTGGATGGCAGGGCTCAGGATATCCATGG
genomic: TTTTTGAGCATCTCCATGgtaagcgcgt ... ttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
EST: gi|149070911|gb|EE159318.2|EE159318
EST:     ATGGTATTTGAATATGCTCCAAATGGGGACACTTTTTGAGCATCTCCATG                         TCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
genomic: ATGGTATTTGAATATGCTCCAAAT-GGGACACTTTTTGAGCATCTCCATGgtaagcgcgt ... ttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
EST: gi|76012816|gb|DT939986.1|DT939986
EST:     GATGGTATTTGAATATGCTCCAAATGGGACACTTTTTGAGCATCTCCATG                         TCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
genomic: GATGGTATTTGAATATGCTCCAAATGGGACACTTTTTGAGCATCTCCATGgtaagcgcgt ... ttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
EST: gi|211162831|gb|FL160688.1|FL160688
EST:     GATGGTATTTGAATATGCTCCAAATGGGACACTTTTTGAGCATCTCCATG                         TCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG
genomic: GATGGTATTTGAATATGCTCCAAATGGGACACTTTTTGAGCATCTCCATGgtaagcgcgt ... ttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacttctgcattgttgatcaaagtttggcaatgccttcctgatttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGGGCATTGCTTACTGTCTTGAGCACATGCATCAGCTGCAAACACCAGCTGC
                                      tcctgat  putative branch site (score: 3)
                                            tttcacc  CT-rich tract
                     aaagttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgcgttgctgtcatgagtttctcagtttcatctgtcacaaaaactgttcttcagcgtgtagagttttatcactatgacttctgcattgttgatcaaagtttggcaatgccttcctgatttcaccgcagTCAGGGAAGCAGAGAAGCTTGACTGGATGGCACGGCTCAGGATATCCATGGGCATTGCTTACTGTCTTGAGCACATGCATCAGCTGCAAACACCAGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC