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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag

Basic information

species Zea mays
transcript GRMZM2G370852_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 8
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
|||||||| || |||||||| |||||||||||| ||||||||||||| ||||| ||||| |||||||| ||| ||||||||||||| || ||||||||||   | | | ||  | |||||||    |  ||  || || |   |  | | |    | ||||  |||| |   || || |   || |    ||||  |||| ||  |   |  ||||| | ||||  |  |  |||| || ||||  ||     ||  | |||||| |||||||
ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAGgtactttaatgg-cctttaaaatgcttggtaataaaatgagcgatatttttatgcaaataaaacaacccaacatccttaagcttc-gaataagaagaaatatttacaagaacaaatttctaacttttacataat--gataattatgactccatatcggtcatcctggta-actgcag

upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G34160.1 (Glycine max), 5'ss of exon 10
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgta--caaaactagtcc---ccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattcca---ataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
||||||||| | |||||||| |||||||||||| | |||||||| || || |||||| | ||  ||||||||  ||| ||||  ||||||||||||||     ||  |   |    || |  ||| |  |  ||   ||   |   |   || ||| |  ||    || ||   |||  |   ||||   || |  |||                                                                                  
ATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAGgttgttgaagttgaacagcgccctttatgtttttctca---tttcactgtttctctcttcatgtatgtgcttgcatatatacatgcaagatgctgaattttca----------------------------------------------------------------------------------

upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||||||       | || |   | | |      |   || |||    | | ||| | |        |  ||   ||  ||      |  | | |     ||     |   |||                                                                    
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgt-------ttgtgcaactgagtagatgcactgaaattga--tattttgcctctaaagttatatgttgtcattggtaaagatttcataatatcttgattgtatcctaga--------------------------------------------------------------------

upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 9
-ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
 ||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||||||       | || |   | | |      |   || ||||     |   || |    | |||   |  || |   |||   |  |    |  | |||  |  ||| |                                                                      
GATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAggt-------ttgtgcaactgagtagatgcactgaaattggtatcttgc-ctctaaagttatatgttctcattggctttctcaatggattttttaagagaagattgta----------------------------------------------------------------------

upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 9
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataa-cattccaataa-gtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
||||||||| | |||||| | |||||||||||||| |||||||| |||||||| |||||| | ||| ||||||  || ||||| || ||  |||||| |   |    |||   ||   | ||  |||            |  ||   ||||||  |  | ||||  | | | || ||   ||             |   | |||||                                                                     
ATGGAAGAAAGAATGACATTGTGCAACATGGTTGTGGAAGCTGGGGGAAAGAATGGTGTCATCCCTCCTGATGCGACGACATTAAATTATGTTGAGgcatgtatactgtcttgtt---ttcttgtaa------------atcatatgtttcttcaaggatcattatattgatgtatgtcttactcctgatcttatatcttctgcag---------------------------------------------------------------------

upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 9
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
||||||||| | |||||| ||||||||||||||||||||||||| |||||||| ||||| || |||||||||   ||||||  ||| ||||||||||| |  ||  | ||   ||   |     ||| |    || || |            || |||| |    || ||    |  | | |   || ||       |||       |    | | || |||| |||||          || |  ||| | |  |||  | |           
ATGGAAGAAAGGATGACATTATGCAACATGGTTGTTGAAGCTGGAGGAAAGAATGGTGTTGTTCCTGCTGATAGTACTACACATAAGTACCTTGAGgt-cggaataaatcagtttctctttctctaatatttgtgtgcta------------ttgataa-acgaaaaaaaaaaaggaacaaaatttgttc-------tttttgtgcttatcatgcaactattttgtttg---------gcttaagtcagtttctttgcacag-----------

upper sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 9
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgt---acaaaactagtccccttaaatgctcataacaaagttgg----gccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag
||||||||| | |||||| |||||||||||||| |||||||||| |||||||| ||||| || |||||||||   ||||||  ||| |||||||||||   |  |||  | ||  ||      ||| |  ||   |||     ||||| | | |  | |||  |  | ||    | |  ||| |  |     |  || |   || |    |   |    ||  ||                                                       
ATGGAAGAAAGAATGACATTATGCAACATGGTTATTGAAGCTGGGGGAAAGAATGGTGTTGTCCCTGCTGATAGTACTACACATAAGTACCTTGAGgttagaagaaatcattcatctctctctctc-tctcatgcttgctattgccaaaagggtgattttttttctctttatgctta--ttgtgcaactctttcttctggctaagtcattg---tttctttgcacag-----------------------------------------------------

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|16916456|gb|BM072849.1|BM072849
EST:     ACTACATTTAAATA-CTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
genomic: ACTACATTTAAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
EST: gi|32840108|gb|CD979789.1|CD979789
EST:     GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
genomic: GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
genomic: GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
EST: gi|32846022|gb|CD985703.1|CD985703
EST:     GAAAGAACGGTGTCGTGCCTGTTGATGAAACTACATTTAAATACCTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
genomic: GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
genomic: GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
EST: gi|211350370|gb|FL368852.1|FL368852
EST:     AAATACCTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
genomic: AAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTCACGCCAG
genomic: GAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaact ... tatactgcagGGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag

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