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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcccttggatagctctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtag

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgt--ctgcc--tcccttgga----------tagctctttaacaattttctt----ggattttggtttaaatagatatcctgtataatctgtag
||| | || ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| || |||||||| || ||||||||||  ||||   || | ||||          ||||| || ||    ||||||    || ||| | |  || |||||    || ||   ||| ||
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 49
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgc--ctcccttggatagctctttaacaattttcttggattttggtttaaa-------tagatatcctgtataatctgtag----------
||||||||||| || || ||||| |||||||||||||| || ||||| ||||||||| | ||  | |||||  |||||||||| |||||  ||||||||| |    ||   ||||||||   |    |   ||| ||   |||   | ||||       ||||    || | || | | ||           
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatataactttgttggatagagttactgcttcttttttttttttccttataaaataaaactagaaccactttttattttctaatgttgtatag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 48
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcccttggatagctctt-taacaattttcttggattttggtttaaatagat----atcctgtataatctgtag--------------
||||||||||| || || ||||| |||||||||||||| || ||||| ||||||||| | ||  | |||||  |||||||||| |||||  ||||||||| |   |  ||| | | | |    | || | | || |   |||      ||| | |     |||   |||  ||| | |              
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 5'ss of exon 48
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcccttggatagctctttaacaattt-----tcttggattttggtttaaatagatatcctgtataatctgtag----------------------------------------
 | || || || || |||||||||||||| |||||| || |||||||||| |||||| | ||| | ||||| |||||||||||||| ||||| || ||||    |||  |       |||||  | | |||     |||  |  | |   |||  | || ||  |   || |  | |                                         
CTCCTCCAAAGCACCATATATGAAGTTGATCTTGATAGACTTCTTCAGAGTATCCATGTATATCTGCAAGATCTGGGAATGGAAGAGATACGTAGGAGgtacatctctttaaatgcactcttagaaattttgcaaatctatgtctgtttattatgtggagatttttcgtacttggcaatactaatgcattctcggttggtattttttccaatgaaaag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 18
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcccttggatagctctttaacaatttt----------cttggattttggtttaaatagatatcctgtataatctgtag-----------------------------------------------
|||||||| ||||| |||| ||| ||||||||||| || || ||||| || || ||| | ||  | |||||| ||||||||||||||||  | ||||||| | |||    |    |  |    || |||||            |||  |||| |   |   || |    | ||| ||  || |                                               
GTTCTTCAAAGTACTATATTTGATGTTGACCTTGACCGCATCCTTCAAAGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAGgtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttcttttggctgttacaatgaaatgaactaccataag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 5'ss of exon 47
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcc--tcccttggatagctctttaacaattttcttggat----tttggtttaaatagatatcctgtataatctgtag------------------------------------------------------------------------------------------------
||||||      ||  |   |||||| |||||||||||||||||||| ||||| ||    |||||  |||| |||||||||| ||||||||||| | |||  |    |  |   | | | ||   |  |  |||     ||    |  | ||| | ||||| |  |  | ||  | | |                                                                                                
GTTCTTGGTTCAACTTTGCTTGAAGTAGACCTTGATCGAATTCTTCAAAGCATTCACGAGTATTTTGAAGAGCTGGGAATGGCAGAAATACGGAAACGgtaagatgatttccgagctcgttcaccacaacgtttgcaatataatatccgtttttactagat-tgttaaaaaagttcttgcgtcgctggctctgagattttagttgactgctattccgttcacggccgtttggttattaacttgatatgtaatgcatgggaatgtctctggatcag

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|18450668|gb|BM428946.1|BM428946
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|87152573|gb|DY397362.1|DY397362
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     GCATCCATATTTATTTANCA-GAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGGTCAAA-CCGTCTTGCATG
genomic: GCATCCATATTTATTTA-CAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGG-TCAAAACCGTCTTGCATG
EST: gi|22489973|gb|BU049896.1|BU049896
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|32851907|gb|CD991588.1|CD991588
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|19822797|gb|BQ048821.1|BQ048821
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST: gi|19822549|gb|BQ048573.1|BQ048573
EST:     AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 42

GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 62

GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 72

GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcccttggatagctctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA