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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactctagatcggctactttctgagtctgcatgtttaacttaatgcattatcctgttttagctaacaactaaactaatggtagtgtcatcttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG

Basic information

species Zea mays
transcript GRMZM2G138861_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 7
aaactctagatcggctactttctgagtctgcat-gtttaacttaatgca--ttatcctgttttagctaacaactaaa--ctaatggtagtgtcatcttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG
    | ||  |    | |||  |     ||| | |||||  ||   |||  || | |    || |||  |    |||  || |||  |||||||| ||  |  ||||||||||||||||||||||| |||||||||| |||||| ||||||||||||| || |||||||||||||||||||||||||| || |||||  ||  |
gttatataatttcttttcttatttctcttgctttgtttacattggagcacttttttcatccttggctctctgtgaaaagctgatgtcagtgtcatttttgtgcagCGTATCTTGAATGTTCAGTACTCAATTCCAGAAAACGTGGACATATCTCCAGAATGTAGGCATCTAATTTCGAGGATTTTTGTCGGGGATCCGTCTTTG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 7
aaactctagatcggctactttctgagtctgcatgtttaacttaatgcatta-tcctgttttagctaacaa--ctaaactaatggtagtgtcatcttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG
               ||  |  |||  ||   | ||| |   ||||   || |  || || |  ||      ||||| | |||  | |||    | |||  || | || ||||||||||||||| ||||||| ||| ||||  |||||||| | |||||| | ||||| || || ||||||||||| |  |||||||| | |
--------------gtaactaatgacactt--tttttcaaccaatgtggtacttttgattgaattagttttcctaaattgatg--aatgt----tggttgcagAGGATTTTGAATGTTCAGTACTCAATTCCTGACTACGTTCACATATCTTCCGAGTGCCGTCATCTGATATCAAGGATTTTTGTCGCTGATCCTGCAAGG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 7
aaactctagatcggctactttctgagtctgcatgtttaacttaatgcattatcctgttttagctaacaa--ctaaactaatggtagtgtcatcttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG
             |  |||   ||   ||   | ||| | | | ||  |||   || || |  ||      ||||||| |||   |      ||||||  || | || ||||||||||||||| ||||||| ||| | ||  | |||||| | |||||| | ||||| || || |||||||||||||  |||||||| | |
-------------gtaactaattgcacctt--tttttcaatcagtgtgttactttgattgaattagttttcctaaactgatgcatg------cttgttgcagAGGATTTTGAATGTTCAGTACTCAATTCCTGACTATGTTCATATATCTTCCGAGTGCCGTCATCTGATATCAAGGATTTTTGTTGCTGATCCTGCAAAG

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|211499758|gb|FL295246.1|FL295246
EST:     ATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
EST: gi|60348192|gb|DN215165.1|DN215165
EST:     ACTTCCGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: ACTTCCGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
EST: gi|6095661|gb|AW120328.1|AW120328
EST:     TAAG-ACTTCCGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: TAAGAACTTCCGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
EST: gi|149009071|gb|EE153785.2|EE153785
EST:     ATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
EST: gi|30087423|gb|CB885629.1|CB885629
EST:     CGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: CGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
EST: gi|31357636|gb|CD441993.1|CD441993
EST:     ATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
EST: gi|149103213|gb|EE288586.2|EE288586
EST:     AGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA
genomic: AGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatctttt ... cttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattatcctgttttagctaacaactaaactaatggtagtgtcatcttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG
                           aactaat  putative branch site (score: 2)
                                         tcatctt  putative PPT
                         taaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactctagatcggctactttctgagtctgcatgtttaacttaatgcattatcctgttttagctaacaactaaactaatggtagtgtcatcttgttatagCGTATCTTGAATGTTCAGTACGCAATTCCAGACAACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT