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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccaatcatattctaaagccaccattgagtctcgatttgttttacttaacatttgtagtcacctatctgtgtgttgcactaactattcttaattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTTCGGACAGCCCATTTGCAGGTGGGGTATTCTTGGTGAACATTCACTTCCC

Basic information

species Zea mays
transcript GRMZM2G102471_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102471_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g57220.1 (Oryza sativa), 3'ss of exon 2
----------atccaatcatattctaaagccaccattgagtctcgatttgttttacttaacatttgtagtcacctatctgtgtgttgcactaactattcttaattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTTCGGACAGCCCATTTGCAGGTGGGGTATTCTTGGTGAACATTCACTTCCC
           |  |||||  |||||    ||  ||| |  ||  | |   | |    || ||||||  | ||  ||||  ||| || |||| || || |   |||||||||||||| |||||||||||||||||||||||||| || || ||||| || || |||||||||||||| |||||||||||||||||||||||||| |||||
cctgcttaatcttgaatcactttcta----cattatttaaactgaactc--tatgtccaaaatttgtt-ttactcatct-cgtgctg-acta-cttttgtctgttgtcagGTCCTGTGGGTGAGGACATGTTCCATTGGCAAGCTACTATTATGGGACCCTCAGACAGCCCATTTGCTGGTGGGGTATTCTTGGTGAACATTCATTTCCC

upper sequence: GRMZM2G102471_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G18310.1 (Glycine max), 3'ss of exon 2
atccaatcat---attctaaagccaccattgagtctcgatttgttttacttaacatttgtagtcacctatc-tgtgtgttgcactaactattcttaattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTTCGGACAGCCCATTTGCAGGTGGGGTATTCTTGGTGAACATTCACTTCCC
||  ||  ||   |  | | |   |  ||||| | |    ||||  |  |  |  | ||  |   | |||| ||  | ||       | |||||| | |   ||| ||||||||||| |||||||| ||||||||||| || || ||||| ||  | ||||| || | ||| ||||| |||||| |||||| ||||||||||||
atataaaaatggaaaacaatatgtaatattgaatattaccttgtagttatgtatctatg-ggaagcttatcatgaatcttatgtattccattcttgagt---agGCCCTGTTGGTGATGACATGTTTCATTGGCAAGCTACAATTATGGGTCCAACTGACAGTCCTTATGCTGGTGGTGTATTCCTGGTGACCATTCACTTCCC
















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|87152240|gb|DY397029.1|DY397029
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|18963462|gb|BM660448.1|BM660448
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211340925|gb|FL033475.1|FL033475
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCRG                         -TCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|32915121|gb|CF019933.1|CF019933
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGC
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGC
EST: gi|19057772|gb|BM736439.1|BM736439
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|20300917|gb|BQ163860.1|BQ163860
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211238217|gb|FL033363.1|FL033363
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211340936|gb|FL033486.1|FL033486
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCYATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|15005359|gb|BI325426.1|BI325426
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211343318|gb|FL033490.1|FL033490
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         -TCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|32801349|gb|CD953585.1|CD953585
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211244923|gb|FL033410.1|FL033410
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGNTGGTGAGGACATGGTCCATTGGNAAGGGAC-ATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211340938|gb|FL033488.1|FL033488
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         TTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|78027527|gb|DV495914.1|DV495914
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211242691|gb|FL033398.1|FL033398
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGGCCT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGG-CCT
EST: gi|6826976|gb|AW330619.1|AW330619
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATT
EST: gi|20301187|gb|BQ164130.1|BQ164130
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211251617|gb|FL033447.1|FL033447
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCAT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211340933|gb|FL033483.1|FL033483
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCAT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|211240452|gb|FL033374.1|FL033374
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCAT
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|78084134|gb|DV512527.1|DV512527
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTC
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTT
EST: gi|78105419|gb|DV523837.1|DV523837
EST:     GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG                         GTCCTGTTGGTGAGGACATGTTCCATTGGCAAG
genomic: GAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAGgtgatttact ... taattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaacatttgtagtcacctatctgtgtgttgcactaactattcttaattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTTCGGACAGCCCATTTGCAGGTGGGGTATTCTTGGTGAACATTCACTTCCC
                                      ctattctt  CT-rich tract
                                   taactattcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccaatcatattctaaagccaccattgagtctcgatttgttttacttaacatttgtagtcacctatctgtgtgttgcactaactattcttaattgtcagGTCCTGTTGGTGAGGACATGTTCCATTGGCAAGCGACCATCATGGGGCCTTCGGACAGCCCATTTGCAGGTGGGGTATTCTTGGTGAACATTCACTTCCC

- ccaatca
- - - - - - - - - -ccaccat
- - - - - - - - - - - - - - - - - - - - - - - - -acatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca