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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatttaacatgttactctaagttgtatgttaatcactgttcatttgctgtttatgtggttgattacatggctgatctaaggaatactgttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG

Basic information

species Zea mays
transcript GRMZM2G101698_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101698_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56310.1 (Oryza sativa), 3'ss of exon 2
tagatttaacatgttac-tctaagttgtatgttaatcactgttcatttgct-gtttatgtggttgatt--acatggctgatctaaggaatactgttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG
    |  |   |||||  |||       | |  ||||| ||  |||   || |||| |||||   | |    |  | |  ||| |  |||  || ||||| ||| || || |||||||| || |||||||| || ||||||||||| ||||||||||| || ||||||||||| ||||||               
----tgcattttgttaagtctggaagtaaagaaaatcaatgcacatgcacttgtttgtgtggcaaaattagtacagattgtctgacaaatgttgctcttttcagAGTGGACTATGTTGTACTGACCAGTGTTGACAGAGATGACTTGCCTGATGGTGGTAGCAGCCATTTTGCGCAGACA---------------

upper sequence: GRMZM2G101698_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G42600.1 (Glycine max), 3'ss of exon 4
--tagatttaacatgttactctaagttgtatgttaatcactgttcatttgctgtttatgtggttgattacatggctgatctaaggaatactgttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG
   || |  ||    |   | ||   ||    |  ||        | |     |||||  | |    | |   ||| || ||     |||  || ||| |||||| ||| || |||| ||||| ||||| ||| | |||||  | |||||||| |||||| |||||||||||||||| || |||||| | |||
acaagttacaatgcctagatttatcatgggcatatattgtgtgctactaaaactttattagatctcattccctgctaat-tacaagctaccatt-tttgcagTGTGGAT-ATATTGTCCTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG

upper sequence: GRMZM2G101698_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 2
tagatttaacatgttactctaagttgtatgttaatcactgttcattt---gctgttta---tgtggttgattacatggctgatctaaggaatactg--ttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG
        ||| |||||  |   | |  || | ||     |  ||||   |||| | |   | |  | |||  |||  |   |  |    |  ||   || ||| ||| || |||||| ||||  |||| ||||| ||| | |||||  | |||||||| |||||| |||||||||||||||| || |||||| | |||
--------acaagttacaatgcctagattgatcatgggcatatattttgtgctgctaaaactttattagatctcattccctgttaattacaagctaccttttttgcagCGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG

upper sequence: GRMZM2G101698_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 3'ss of exon 2
tagatttaacatgttactc-taagttgtatgttaatcactgttcatttgctgtttatgtggttgattacatggctgatctaaggaatactgttctt-----tccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG
     |   | ||||      ||| || || | |   ||   |  |||| | | | | |  |   || | |||   ||   | ||||  || | ||     |  ||||| |||||  |||| ||||| ||||| ||| | |||||  | ||||||||||||||| |||||||||||| ||| || || ||| | |||
-----tatgcgtgttttagacaagatgcatatgatctacaaattttttggtatgtttattat-acttgcttggaaaattataagaattttgattttcattttgtagTGTGGATTACATTGTTCTAACAAGTGTTGATCGTGATGATCTGCCTGATGGTGGAAGTGGCCATTTTGCTCGGACTGTTAAGGCTATGAAG

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|32859726|gb|CD999407.1|CD999407
EST:     CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGG                         TGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG
genomic: CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGGgtatgatctc ... ttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG
EST: gi|67023528|gb|CO452277.1|CO452277
EST:     CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGG                         TGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG
genomic: CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGGgtatgatctc ... ttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG
EST: gi|149001281|gb|EE038564.2|EE038564
EST:     CCTGATCCCCTGAAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGG                         ---A--TTATGTTGTGCTAACCAGTGTCG
genomic: CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGGgtatgatctc ... ttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCG
EST: gi|78112107|gb|DV530503.1|DV530503
EST:     CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGGTGCAAGCTGGGG                         TGTAGATTATGTTGTGCTACCCAGTGTCGATAGAGATGACTTACCTGATGG
genomic: CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGGgtatgatctc ... ttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG
EST: gi|71324730|gb|DR799071.1|DR799071
EST:     CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGG                         TGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG
genomic: CCTGATCCCCTGGAGCCTCTGAACACGGCTTTGGCTGTTGCAAGCTGGGGgtatgatctc ... ttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgtttatgtggttgattacatggctgatctaaggaatactgttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG
                         ggctgat  putative branch site (score: 4)
                                          ctgttctttcc  putative PPT
      tttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatttaacatgttactctaagttgtatgttaatcactgttcatttgctgtttatgtggttgattacatggctgatctaaggaatactgttctttccagTGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG