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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacgtagattttcttcagaaatcagaatatggttgttgtatggctaagttgttgttgtgttgctaatttttttatgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG

Basic information

species Zea mays
transcript GRMZM5G825110_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 7
gttacgtagattttcttcagaaatcagaatatggttgttgtatggctaagttgttgttgtg------ttgctaatttttttatgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG
|| |  ||   |||| |  | |||  || | ||   ||||| |    || ||| |  ||||      ||  ||  ||| | | |||||| ||||||||| ||||| || |||||||||  |||||| |||||||| |||||||||||||| ||||| || |||||||| | ||||||| |  ||
gtgagatatcatttcctttggaatgtgattgtga--gttgtctacacaatttgctactgtgattcttttcttatatttatcacgcaaatgatttcagGACCTGTCGACAGGGTGGCTTCGTTGTGACCCTGGTCCTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 7
gttacgtagattttcttcagaaatcagaatatggttgttgtatggctaagttgttgttgtg------ttgctaatttttttatgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG-------------
|| |  ||   |||| |  | |||  || | ||   ||||| |    || ||| |  ||||      ||  ||  ||| | | |||||| ||||||||| ||||| || |||||||||  |||||| |||||||| |||||||||||||| ||||| || |||||||| | ||||||| |  ||             
gtgagatatcatttcctttggaatgtgattgtga--gttgtctacacaatttgctactgtgattcttttcttatatttatcacgcaaatgatttcagGACCTGTCGACAGGGTGGCTTCGTTGTGACCCTGGTCCTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGGGTAAGAACATTGA

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G02210.1 (Glycine max), 3'ss of exon 5
gttacgtagattttcttcagaaatcagaatatggttgttgtatggctaagttgttgttgtgttgctaatttttttatgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG
     ||| |   |||| |       |  |   ||  |  ||||   || |  || |  |||| |||||  |  |    |||||| |||||||| | |||||||| |||||| | ||||| ||||  ||||| |||||||||||  |     |||||  ||  | | |  | ||||||
-----gta-acaatcttga-----ttgggtgctgtcatc-tatgaggaaatatttatgatgttcctaatgatggtg---aaataaattcagGATTTATCAACTGGTTGGCTTCAGTGTGACCCTGACCCAATTTTTAAGCCAGATTACATTCCATTGCCAGGATTGATTTCTCATTGG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 7
gttacgtagattttcttcagaaatcagaatatggttgttgtatggctaagttgttgttgtgttgctaatttttttatgcaaataat-ttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG
     ||| |  |  || | | |    ||     || ||  |   | || |   |       |||| |  | | | ||  |||||  |||||||| |||||||||| |||||| | ||||||||||||||| |||||||||| ||   |||  | ||   ||  | | |  | || |||
-----gtataactaattgatataatgtaaggca-ttattcaacaacaaactgact-----aatgctcacatctctttgggaataacattcagGATTTGTCAACTGGTTGGCTTCACTGTGATCCTGGTCCACTGTTTAAGCCGGAATCTTATCCCTTACAAGGATGGATTTCCCACTGG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 7
---gttacgtagattttcttcagaaatcagaatatggt----tgttgtatggctaagttgttgttgtgttgctaatttttttatgcaaataat-ttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG
   | |  ||| || | | | |  |||    |||| ||      || |    | ||    |   |    |||| |  | | | ||  || ||  |||||||| |||||||||| |||||| | ||||||||||||||| |||||||||||||   |||  | ||    |  |   |  | || |||
gtagctctgta-atatacataactaattgatatattgtaaggcattattcaacaaaaaactgactaa--tgctcacatctctttgggaacaacattcagGATTTGTCAACTGGTTGGCTTCACTGTGATCCTGGTCCACTGTTTAAGCCAGAATCTTATCCCTTACCTGGATGTATTTCTCACTGG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 7
gttacgtagattttcttcagaaatcagaata-tggttgttgtatggctaagt-tgttgttgtgttgctaattttttt-atgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG
     |||  | ||    |  |||   | |  | |  |  | ||   |     | ||    | |   |||||||| | || ||| | ||  |||||| | |||||||| |||||| ||||||||||||||||  |||||||||||||| ||| |   ||   ||  | ||| ||    |||
-----gtaagtatttcagatgaatattactccttgaagaagcatatttgtccatcttcagatatgcttaatttttgtgatacaattcatg-cagGATTTATCAACTGGTTGGCTTCATTGTGATCCTGGTCCGTTGTTTAAGCCAGAGTATTTCGATTTATCAGGATGGGTTCCTAGATGG

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|60338336|gb|DN205309.1|DN205309
EST:     TGTTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAG                         GATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
genomic: TGTTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAGgttacgtaga ... ataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
EST: gi|60344634|gb|DN211607.1|DN211607
EST:     TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAG                         GATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
genomic: TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAGgttacgtaga ... ataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
EST: gi|76014866|gb|DT942036.1|DT942036
EST:     TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAG                         GATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
genomic: TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAGgttacgtaga ... ataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
EST: gi|76021500|gb|DT948670.1|DT948670
EST:     TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAG                         GATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
genomic: TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAGgttacgtaga ... ataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
EST: gi|76287485|gb|DV027053.1|DV027053
EST:     GGCCGTTTCCAATGGTTGACAAGCCCAAGAAAG                         GATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA
genomic: GGCCGTTTCCAATGGTTGACATGCCCAAGAAAGgttacgtaga ... ataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtatggctaagttgttgttgtgttgctaatttttttatgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG
                          tgctaat  putative branch site (score: 2)
                         ttgctaatttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacgtagattttcttcagaaatcagaatatggttgttgtatggctaagttgttgttgtgttgctaatttttttatgcaaataatttcagGATCTGTCAACTGGGTGGCTTTATTGTGATCCTGGTCCAATGTTTAAGCCAGAGCATTACTCATTGGGAGAGTCGGTGCCACATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA