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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcagagatacacaaaaattcagtatttgaaactttgttacttcccaacataaaggtgttggtattcacaaaaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTTGCTCGTGAGTTGATCAAAGAAGAATGTGTCCTGGTTCTACCTG

Basic information

species Zea mays
transcript GRMZM2G006480_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006480_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g42510.2 (Oryza sativa), 3'ss of exon 8
gttagtc-agagatacacaaaaattcagtatttgaaactttgttacttcccaacataaaggtgttggtattcacaaaaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTTGCTCGTGAGTTGATCAAAGAAGAATGTGTCCTGGTTCTACCTG
||| |||   ||||| ||  |  || |||| ||   | |   ||| | |     || |  |  | | |  || ||||| | | ||||||||  ||||||||||| ||||    || || |   | ||||||||||| |||||||| ||||| |||||||||| |||||| ||| ||||||
gttggtctgaagataaactgat-ttgagtaattcctaatgatttattgctt--tatcattgaatcgatgctctcaaaatcattcagGTTGAAGTCAACACTTCACTTCTGTTCGGTGTTGAAGATGACATGGACTTCGCTCGTGAATTGATTAAAGAAGAATCTGTCCTAGTTTTACCTG
















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|148953483|gb|EE152988.2|EE152988
EST:     TCGAAGCCCTGCGGTGGTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTTTACATGGGGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|67020982|gb|CO449731.1|CO449731
EST:     TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|211097014|gb|FL478914.1|FL478914
EST:     TCGAAG-CCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|86473866|gb|DY240236.1|DY240236
EST:     TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTTTACATGGCGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|76289527|gb|DV029095.1|DV029095
EST:     TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|78089839|gb|DV518213.1|DV518213
EST:     TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|76911586|gb|DV164332.1|DV164332
EST:     TCGAAGCCCTGCGGTGGTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTTTACATGGGGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
EST: gi|8102634|gb|AW927434.1|AW927434
EST:     TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATG                         GTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT
genomic: TCGAAGCCCTGCGGTGCTACTCCAAGCCTGAAGGCTCAATGTTTATGATGgttagtcaga ... aaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaactttgttacttcccaacataaaggtgttggtattcacaaaaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTTGCTCGTGAGTTGATCAAAGAAGAATGTGTCCTGGTTCTACCTG
                    aacataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcagagatacacaaaaattcagtatttgaaactttgttacttcccaacataaaggtgttggtattcacaaaaccctgcagGTTGAGATCAACACTTCAATTCTACATGGCGTCGCCAACGACATGGACTTTGCTCGTGAGTTGATCAAAGAAGAATGTGTCCTGGTTCTACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG