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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

Basic information

species Zea mays
transcript GRMZM2G370852_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
gtgcgttccctgctcaagattatcttaattaattg---ccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
||  | ||| ||||||  | ||  || || ||||     ||     | |  | || ||| || |  ||| | |||||||| ||||||||||| || |||||||| |||||||||||| ||||||||||||| ||||| ||||| |||||||| ||| ||||||||||||| || ||||||
gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
--gtgcgttccctgctcaagattatcttaattaat----tgccacaccacgtaacattgaacttagtccttttcacaaact-tgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
   ||| | |  |   ||   || ||||  |  ||    ||  |       ||  ||   ||||     || |   |   | |  |||||||||||| | |||||||| |||||||||||| | |||||||| || || |||||| | ||  ||||||||  ||| ||||  ||||||||||||
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 8
--------------------gtgcgttccctgctcaagattatc-ttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                     |   ||      ||||  | |    |  ||  ||   |    |  ||| | |    || ||  |||   |    | | |||||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||| 
aaaacacaagtaaacgggccataaatttttc-ttcaatctcagaactctttcttttttattataaataaaagttgttttggtaatttgttcctcttggataGATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGA-

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 8
--------------------gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                          |   |  ||||  |        ||  ||   |    |  ||| ||||   || ||  |||   |    | | |||||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||||
gaaaacacaagtaaacgggccctaaatttttcttcaatctcggaactctttcttttgattataaataaaattgt-tttggtaatttgttcctcttggatagATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------gtgcgttccctg-ctcaagattatcttaattaattgc--cacaccacgtaa-cattgaact-tagtccttttcacaaactt---------gctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                              || || || |  || |     ||   ||||||| ||  || |  | || | ||||||  | ||     || |   ||  |         |||||||||||||| | |||||| | |||||||||||||| |||||||| |||||||| |||||| | ||| ||||||  || ||||| || ||  |||||
gtaagaaatcattctatatttcctacattatgggtcccttctcttatagaaataaaaattaatagctgcatatgatgttatcattgatttataaatggttgcttgaatcttttttggctgctagATGGAAGAAAGAATGACATTGTGCAACATGGTTGTGGAAGCTGGGGGAAAGAATGGTGTCATCCCTCCTGATGCGACGACATTAAATTATGTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------gtgcgttccctgctcaagattatcttaattaat-tgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                                              || | || | ||      |||   ||||| |   ||        |  |   ||||  |   || || |   |||||    ||||||||||| | |||||| |||||||||||||| |||||||||| |||||||| ||||| || |||||||||   ||||||  ||| |||||||||
gtaggtgcacttttatagatcttccactgcaagtatctaaatcactgttcatttc-tgtgtggaatttgtttaatcagcctgttctggatcacagttttga-ttgtttcattgttctaaactgaaaagATGGAAGAAAGAATGACATTATGCAACATGGTTATTGAAGCTGGGGGAAAGAATGGTGTTGTCCCTGCTGATAGTACTACACATAAGTACCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------------gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                                                ||| || | | || ||  || | | |   || |||         |    || |   |  |  |  || ||| ||    ||||||||||| | |||||| ||||||||||||||||||||||||| |||||||| ||||| || |||||||||   ||||||  ||| |||||||||
gtaagttcacttttacagatcttcccctgcaaaaatctcaagtcattctgcatttctttctgaaatttgtataatcaaactgcactggattatggttttaattgttttattcctctcaa-ctgaaaagATGGAAGAAAGGATGACATTATGCAACATGGTTGTTGAAGCTGGAGGAAAGAATGGTGTTGTTCCTGCTGATAGTACTACACATAAGTACCTTGAG

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|32840108|gb|CD979789.1|CD979789
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
EST: gi|32846022|gb|CD985703.1|CD985703
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCGACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAA
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAA-CCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAA
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                acgtaac  putative branch site (score: 3)
                   taacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT