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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtattgctgtatttgcaaaggctggcatgattgttgccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG

Basic information

species Zea mays
transcript GRMZM2G128688_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 1
agtattgctgtatttgcaaaggctggcatgattgttgc--cgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgctttt--agGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
  | |||     | | ||  |  |||    || | |||   | ||  || |||  | |     | |   ||| | |   ||  |  | | ||||  || |  ||||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||| || 
--tgttgaaacttcttcattga-tggtccaatagctgcatagcattcagtatggta-actttttatgtggcatctcacttttttcgtctcggctatttgtgtagGTCACTTCTGTCTCTTGGAAGGAGAACGAACTCAACATGGTTGATACACCTGGTCACGCTGATTTTGGTGGCGAA

upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 1
------------agtattgctgtatttgcaaaggctggcatgattgttgccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
            | |     | | ||  |     | |    | ||     || || |   ||    | ||| |        | ||||  |   || | |    |  ||| ||||||| ||||| || |||||||| ||||| || |||||||||||||| || || ||||| |||||||||||||||
gtccctgccctaatttcaattcttttcaccctctccgcttcgttttcaatcgaatcgg--atcttctttgagaatccggaaagcactaatgaatgct-tcaatt--tttcagGTCACGTCTGTTTCGTGGAAGGAGAATGAGCTGAACATGGTTGATACTCCCGGGCACGCCGATTTTGGTGGTGAG

upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 1
agtattgctgtatttgcaaaggct--ggcatgattgttgccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
     |||  || || | |    |    | |    | | |  | |  | |    |  ||        | |||| |  | |  | | || | |    ||| ||||||| ||||| || |||||||| ||||| || |||||||||||||| || || |||||||||||||||||||||
gtccctgccctaatttccagtttttcaccgtctccggttcgttttcaatcgaatcggatcttcgagaatgcaaaagcgttaac-ggtgcttgaatttttcagGTCACGTCTGTTTCGTGGAAGGAGAATGAGCTGAACATGGTTGATACTCCCGGACACGCTGATTTTGGTGGTGAG

upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 1
agtattgctgtatttgcaaaggctggcatgattgttgccgtatagagcatgccatatgaa-atcttaagcaacactgcttgctgatgttggctgcttt--tagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
   ||  |||||  |  |   | |    |     || ||  | |     |    ||| |  |  |||  | ||| |    | | ||||    |  |     |||| || ||  | | ||||||||| || ||||| |||||||| || |||||||| ||||| |||||||||||||||
---atgtctgtaacttgatgtgttcttttaccgattccctgagattttgttatttatcaccacgttacacgacatttaaagtttatgtcaaattttccgacagGTGACATCAATATTTTGGAAGGACAACGAACTTAACATGGTAGACACACCTGGTCACGCAGATTTTGGTGGTGAG

upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 1
agtattgctgtatttgcaaaggctggcatgattgttg-ccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
  ||| |   |  ||| |  |   |    |||        |  | ||   | |  |       |  | ||   | | ||      | |    |  ||  |||| ||  |  | |  ||||||||||| ||||| || |||||||||||||| ||||| || || ||||||||||| 
tttatgggctttcttgtatggttggattggatcaccaattgctttgattgttctttccatccccaaacgctttatt-ctattccctatcaattatttgcagGTTACGGCCATTTTGTGGAAGGAAAACGAACTAAATATGGTTGATACACCCGGCCATGCGGACTTTGGTGGTGAA

upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 1
agtattgctgtatttgcaaaggctggcatgattgttgccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttg-gctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
                                       ||||   ||||  | | |    | ||      |       ||| |   || |||  |  |||   |||||| |    |||      | |   |||||||| |||||||| ||||| ||||| ||||||||||| |||
---------------------------------------gtat---gcat-tcgttttttttttttttttccttcttgcgctaagagtgtgctcttggtagTATACTTCTATGATCTGGGGAACCAGTTCTCTCAACATTGTTGATACTCCTGGTCACGCAGATTTTGGTGGAGAG

upper sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15282 (Selaginella moellendorffii), 3'ss of exon 1
agtattgctgtatttgcaaaggctggcatgattgttgccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
                                       ||||  |    |   | |    | ||   |  |      |     |||  |||  |   ||   |||||| |    |||      | |   |||||||| |||||||| ||||| ||||| ||||||||||| |||
---------------------------------------gtatgcatt-cgtttttttttttttttttcttcttgcgctaagagtgtgtgctcttggcagTATACTTCTATGATCTGGGGAACCAGTTCTCTCAACATTGTTGATACTCCTGGTCACGCAGATTTTGGTGGAGAG

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|30705082|gb|CD058659.1|CD058659
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|149065568|gb|EE286688.2|EE286688
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|149096163|gb|EE181859.2|EE181859
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|94477374|gb|EB706332.1|EB706332
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|71428852|gb|DR809902.1|DR809902
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|149075128|gb|EE163621.2|EE163621
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG
                                 tgctgat  putative branch site (score: 3)
                                             ctgctttt  putative PPT
        atatgaaatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtattgctgtatttgcaaaggctggcatgattgttgccgtatagagcatgccatatgaaatcttaagcaacactgcttgctgatgttggctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- -attgctg
- - - - - -atttgca
- - - - - - - - - - -gctggca
- - - - - - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - -agcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg