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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

Basic information

species Zea mays
transcript GRMZM2G079538_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
gtatttgccagtcttaggcgttgc------aaagcttttgcaccatactttt--------atgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
||| |  ||| ||||  |   |||        | || ||||    || ||||        ||       |||  ||  ||||| ||||  ||||||||||| | |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
--gtatttgccagt--cttaggcgttgcaaagcttttgcaccatacttttatgtggctg---gctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
   | ||| | | |  || | |  | |   ||||       |    ||| || |         ||  ||||  |     || ||||||||||||  |||||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||||| ||  |||| |||||  | |||||||
gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 12
--gtatttgccagtcttaggcgt-tgcaaagcttttgcaccatacttttatgtggctg-gctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
   | ||| | | |    |   | |  |     |  ||    | |||| || |       ||  ||||  |     || |||||||||||   |||||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||||| ||  |||| |||||  | |||||||
gtatgttttctaattactgaaatataaactagctgggctttctcctttgatttcctcatactttttatggtctccatgttagGCTGCTGTCAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
------------gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatg--tggctggctaattatatttgttt-tggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
             |||||  |  | |||     | ||| ||    |    ||  |   |    |      ||| |  |  || | | |   |||||||||||   || |||||  | || ||| |||| ||||| || ||||| || ||||| ||||||||||||||||| || || |||||| | |||||||
gtatacacttacttatttttcgatattaa-taatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggcta--attatatttgttttgg----tagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
                    |  ||  || ||   |        |  |    ||      | ||| || ||||||   ||    ||| || |||    ||||| |||||   ||||||| |  |    ||    || ||||| || || ||||| ||||| |||||||||||||||||| | ||||||||  |||||||||
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctat-tgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
-----------------gtatttgccagtcttaggcgttgcaaagcttttgc--accat--acttttatgtggctggctaattatat-ttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
                          |  | || ||    ||   ||  ||   | ||   |||  ||      || | | ||   | |||  ||   |||| || ||   ||||||  |  |    ||   |||||||||||| |||||||| ||||||||||| ||| |||| ||||| ||||||||  |||||||||
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ31629 (Selaginella moellendorffii), 3'ss of exon 6
gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
          || || ||||| |  |     |    | | | |||  | | |||| |  |    ||||       ||||||||||||   ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||||||||  |||||||||
----------gtattcggcgtgg--attgcgtaattcaagagtttctttttgctgacagacgtcattt-------tagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

upper sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
          || || ||||| |  |    ||    | | | |||  | | |||| |  |    ||||       ||||||||||||   ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||||||||  |||||||||
----------gtattcggcgtgg--attgcttaattcaagagtttctttttgctgacagacgtcattt-------tagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

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|211104575|gb|FL031921.1|FL031921
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|31358903|gb|CD443260.1|CD443260
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|211169880|gb|FL077609.1|FL077609
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|32830086|gb|CD969764.1|CD969764
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|13558100|gb|BG549456.1|BG549456
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|32942914|gb|CF047733.1|CF047733
EST:     TGTCACAAAGCATGGTGTAAAATTGG-TCCTCATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TGTCACAAAGCATGGTGTAAAATTGGGTCTT-ATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|60358853|gb|DN225826.1|DN225826
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|6227238|gb|AW155837.1|AW155837
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|32829046|gb|CD968724.1|CD968724
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|32828877|gb|CD968555.1|CD968555
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|211169873|gb|FL077602.1|FL077602
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|13558537|gb|BG549893.1|BG549893
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|32867030|gb|CF006712.1|CF006712
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
EST: gi|67019048|gb|CO447797.1|CO447797
EST:     TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG                         GCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgcca ... gttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagcttttgcaccatacttttatgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
                               ggctaat  putative branch site (score: 3)
                                          tttgtttt  putative PPT
                                  taattatatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT