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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatttgtttcacactccgatttgaaacaagtgaaatgtttttttcccttggaggagagggagccagatgtgaacttattatctttcttttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCC

Basic information

species Zea mays
transcript GRMZM2G157675_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 3'ss of exon 3
----tctatttgtttcacactccgatttgaaacaagtgaaatgtttttttcccttggaggagagggagccagatgtgaacttattatctttcttttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCC
    | ||| || ||| ||     ||||  | | ||  |    |  ||   |  |  | ||     | | |       | | ||| |  || || |   ||||| |   |||||| ||||| |||||||| ||||||||||| ||| |||||||||||||| ||||||||||||||  ||||||||||||||||||||||||||
ttaatatatatgattc-catcttaatttctagctagctagg-atcattaatcaatataagatttttatctaacaa--gattaattgtgattattatcactgcagGGGAAAGTGATAAAGACGAAGAGCGTGGAGTACATGCCGTTCTTCCTGTCGCTGGTGTGCTTCCTCAACGGCGTCTGCTGGACGGCCTACGCGCTCATCC

upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 3'ss of exon 3
tctatttgtttcacactccgatttgaaacaagtgaaatgtttttttcccttggaggag-agggagccagatgtgaacttattatctttcttttttg-tgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCC
    ||| |||   |   | || | | |  | | |||| | |     | ||  |  |  |   |   |||| | ||   |  |  ||  |   |   ||||| |   |||||| ||||| |||||||| ||||||||||| ||| |||||||||||||| ||||||||||||||   |||||||||||||||||||||||||
--attttctttgttataacaatgttacaatacttaaatttctaggatcattatataattaattaatgagattttaatcaacgagattattcactcactgcagGGGAAAGTGATAAAGACGAAGAGCGTAGAGTACATGCCGTTCTTCCTGTCGCTGGTGTGCTTCCTCAACGGCGTTTGCTGGACGGCCTACGCGCTCATCC

upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G02890.1 (Glycine max), 3'ss of exon 3
------tctatt-tgtttcacactccgatttgaaacaagtgaaatgtttttttcccttggaggagagggagccagatgtgaacttattatctttcttttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCC
      |||||  | |||||     |  ||| ||   ||  |         || |  ||      ||| |   | |||  || |   | |   |  ||   |||||||  |  ||||||||||| |||||||||||||||||||||||   | | || || |     ||    || ||       |||||  | ||  | |||||||
aaaaggtctatggtatttcatttctcacttttaatttagcaa-----ccaattactatgtgcttaaggtaattacatgataatta--tgttgattattgcggtgcagAAACTGGTGATCAAGACTAAGAGCGTTGAGTACATGCCCTTTTACATCTCTCTCGCCTCTTTTGGGAATGGTGTGGCTTGGACAACTTATTCTCTCATCC

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|211162570|gb|FL132729.1|FL132729
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|211162573|gb|FL132732.1|FL132732
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|28188031|gb|CB179641.1|CB179641
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|211388914|gb|FL454573.1|FL454573
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCYTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|31627932|gb|CD526360.1|CD526360
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCC
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCC
EST: gi|28188247|gb|CB179857.1|CB179857
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGGGGTACATGCCCTTTCCTCCCTG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAG-TACATGCCCTT-CCTCC-TG
EST: gi|37361336|gb|CF602625.1|CF602625
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|211162572|gb|FL132731.1|FL132731
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|28566554|gb|CB278202.1|CB278202
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|148934526|gb|EC878568.2|EC878568
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|17932131|gb|BM269091.1|BM269091
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|31628107|gb|CD526445.1|CD526445
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAAAGCGTTGAGTA
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTA
EST: gi|14245092|gb|BG873674.1|BG873674
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|211148276|gb|FL467068.1|FL467068
EST:     CTGCGTCATCTTCGGCTCGATGATGTACGCYTCACCACTYACCTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTC
genomic: CTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCA-CTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTC
EST: gi|71317142|gb|DR795259.1|DR795259
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCCTTC-TCCTGTC
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCC-TTCCTCCTGTC
EST: gi|7138105|gb|AW499432.1|AW499432
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|28188001|gb|CB179611.1|CB179611
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATG
EST: gi|24462465|gb|BM659996.1|BM659996
EST:     TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
genomic: TCTGCGTCATCTTCGGCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG
EST: gi|211124352|gb|FL444992.1|FL444992
EST:     GCTCGATGATGTACGCCTCACCACTVACTATCATG                         AGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTYG
genomic: GCTCGATGATGTACGCCTCACCACTCACTATCATGgtacgtgatc ... ttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccttggaggagagggagccagatgtgaacttattatctttcttttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCC
                              cttattatctttcttt  CT-rich tract
                            aacttattatctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatttgtttcacactccgatttgaaacaagtgaaatgtttttttcccttggaggagagggagccagatgtgaacttattatctttcttttttgtgcagAGTCGAGTGATCAAGACCAAGAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - tgtttca
- - - - - - - - - - - - -aaacaag
- - - - - - - - - - - - - - - - tgaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagcca