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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC

Basic information

species Zea mays
transcript GRMZM2G081848_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081848_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 5
gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC
||||||| |   || |   | || || |    ||||||||         ||  |||  |    |||||||||   ||| |||    |||| || ||||||    ||| ||||| |||||||| ||| |||| || ||||| || |||||||||||||| |||||||||||||| || || |||||||| |||||||| || ||||
gtaagcagt---aaactgagttttggaga---cttatgtt---------gaacgtagctgtgcttcatctgact-cggttct----ttacggtatctgca----gTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC

upper sequence: GRMZM2G081848_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctc--tgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC
|| ||  |   |   || ||  |       | |||||    || |||    |  | ||| ||| ||         |   |  ||   | ||   |   ||  |||||||||||||||| ||||| ||||| || || ||||| |||||||||||||| || ||||| || || || || || ||||| || || || ||||| || |
gtgagactcaatttcccggggattctaccaaacttat----taactgatcttcttgcttccatgtcgatc--ctgcatattaacgagtgcttctttgttgattgcagTTCTTCATCGTCCTGTCTTGCCTCATATCAGTCTCTGTAAACTTCAGCACATTTCTTGTCATTGGAAAAACATCTCCTGTCACATATCAGGTTCTAGGAC

upper sequence: GRMZM2G081848_T03 (Zea mays), 3'ss of exon 6
lower sequence: EFJ14247 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctctgcat--gcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC
                                                 |  || || | | ||| ||| |   | |   |  |  ||  | ||| ||| |  |||| | |||||| | || || ||| |||| || || || || ||||||||||| |||||||| || |||||||||||||| || || ||||||||  | ||||
-------------------------------------------------gtaagcacatgctttttatccgcctatgaaacgcctttttttttctttgcctctgcagCTATTCATCATCCTTTCTTGCTTGATTTCCGTTTCTGTGAACTTCAGCACATTCCTTGTTATAGGGAAGACGTCGCCGGTGACTTACCAAGTCTTAGGCC

upper sequence: GRMZM2G081848_T03 (Zea mays), 3'ss of exon 6
lower sequence: EFJ20116 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctctgcat--gcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC
                                                 |  || || | | ||| ||| |   | |   |  |  ||  | ||| ||| |   ||| | |||||| | || || ||| |||| || || || || ||||||||||| |||||||| || |||||||||||||| || || ||||||||  | ||||
-------------------------------------------------gtaagcacatgctttttatccgcctatgaaacgcctttttttttctttgcctttacagCTATTCATCATCCTTTCTTGCTTGATTTCCGTTTCTGTGAACTTCAGCACATTCCTTGTTATAGGGAAGACGTCGCCGGTGACTTACCAAGTCTTAGGCC

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|149097658|gb|EE183555.2|EE183555
EST:     ACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTG                         TTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
genomic: ACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTGgtaagcattg ... ctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
EST: gi|31358400|gb|CD442757.1|CD442757
EST:     TTTTGACTAACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTG                         TTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
genomic: TTTTGACTAACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTGgtaagcattg ... ctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
EST: gi|32842786|gb|CD982467.1|CD982467
EST:     TTTTGACTAACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTG                         TTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
genomic: TTTTGACTAACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTGgtaagcattg ... ctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
EST: gi|149102836|gb|EE288178.2|EE288178
EST:     TTTGGACTAACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTG                         TTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT
genomic: TTTTGACTAACCAAAACGTCTTTGCTTTCGACTACACAACTCAAGTCCTGgtaagcattg ... ctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtactttcatttcatctgatcacgggtctacacttactgtctctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC
                                 cacttac  putative branch site (score: 2)
                                       ctgtctct  CT-rich tract
       tttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC

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