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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttacttgttggttgcgttttcttcttagttcttacctgcacaatgaagcaatgaacaatggcttaattatgttacctgttcaattcatccctcgc...

Basic information

species Zea mays
transcript GRMZM2G174757_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 5'ss of exon 2
CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtatttt---acttgttggttgcgttttcttcttagttcttacctgcacaatgaagcaatgaacaatggcttaattatgttacctgttcaattcatccctcgc----
 |||||||| ||||| ||||||  |||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||| |||||| |||||| |||   || |||  | ||| ||||   |      ||||   |||  |   |    |  |   | |  |    | || | |  |   ||   | ||        
TCAAATTGGTGCGATCAAAGAAGGTGGTCTTTGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGCTTCATCGAGTATAATACCCCACAGgtactttgccacatgtcagatgcatttttccc------cttaga-gcatgacacatggcttgattcttgtctttgcaagtcatccctcagatctgtaccatttgaac

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G14870.1 (Glycine max), 5'ss of exon 2
CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattt----tacttgttggttgcgttttcttcttagttctta-cctgcacaat--gaagcaatgaacaatggc-ttaattatgttacctgt-----tcaattcatccctcgc----------------------------------------------
 |||||||| |  || || ||  |||| || |||||||| ||  | || || ||  |||| ||    |||||||| ||||||||||| | ||||||||||||||      |  || ||   ||   | |     || || ||  |||  |   |  |  |  |   |   ||   | |||| ||||    ||     |  | |  |   | |                                               
TCAAATTGGTGTTATCAAGGAGGATGGCCTCTGGATGCCGGTTGATCCTGAAACCGAGAAAACCCTAGGTTACTGCTTCATTGAGTACAATACCCCTCAGgtatacacgctctttcttcaatgtaatctaaaaataattgttgtcctatattgtttgttgttagtgattttgatgtcaattgtgtttttagtcgatgttgaattgtatgttgtttttctgatttgggtgtggttaaattgggcgtttattttttcttag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G00470.1 (Glycine max), 5'ss of exon 2
CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttacttgttggttgcgttttcttcttag---ttcttacctgcacaatgaagcaatgaacaatggcttaattatgttacctgttcaattcatccctcgc-------------------------------------------------------------------------------------
 |||||||| |  || || ||  |||| || |||||||| ||  | || || ||  |||| ||    |||||||| ||||||||||| | |||||||||||||   |||  |   | |  || ||  |   |    |  | |||||     |   |   | |   ||   ||||| |||| |  |||    ||       |                                                                                       
TCAAATTGGTGTTATCAAGGAGGATGGCCTCTGGATGCCGGTTGATCCTGAAACCGAGAAAACCCTAGGTTACTGCTTCATTGAGTACAATACCCCTCAGgta---tacacgcacgctcggtctttctaaaaaaattgttgacctgtttgttt--gttgttagtgat--tttaataatgtcaattgtgttgttggaagtgcttttagtcgagatattgaattgtaagtttttgtttttttttttttttatttgggtgtggttaaattgggcgtttgttattttcttag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G06080.1 (Glycine max), 5'ss of exon 2
CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttacttgttggttgcgttttctt---cttagttcttacctgcacaatgaagcaatgaacaatggcttaattat--gttac-ctgttcaat-tcatccctcgc----------------------------------------------------------------------
 || ||||| |  || || ||  |||| || ||||||||| |  | || || ||  |||| ||    |||||||| ||||||||||| | ||||||||||||||      | ||  ||   | | | |   | ||||    | ||  ||||        |    | ||  || | | |   ||    |||| ||  | ||   | |                                                                       
TCAGATTGGTGTTATCAAGGAGGATGGCCTCTGGATGCCTATTTATCCTGAAACCGAGAAAACCCTAGGTTACTGCTTCATTGAGTACAATACCCCTCAGgtatacactctctttcttcaatgtacctggacatagtgaa-atctaaacaaattgtttgttgttagtgattttaatgtcaattgtgttgttgaaagtgatttttagtggatatgatattggattgggtgttgttttttttatttggtgtggttaaattcggtgtttatttttcttag

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|211181447|gb|FL114904.1|FL114904
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACA-GTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|32827808|gb|CD967486.1|CD967486
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|32809690|gb|CD961924.1|CD961924
EST:     AGACAAAGAAGACATACGGTTACTGCTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|78085595|gb|DV513988.1|DV513988
EST:     GACAAAGAAGACATACGGTTACTGTTTCATTTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: GACAAAGAAGACATACGGTTACTGTTTCATT-GAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|211183849|gb|FL114917.1|FL114917
EST:     AGACAAAGAAGACMTACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAG
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAG
EST: gi|149098249|gb|EE184215.2|EE184215
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|9952026|gb|BE638609.1|BE638609
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACGCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|211020785|gb|FL433473.1|FL433473
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|211181453|gb|FL114910.1|FL114910
EST:     GACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCCAG                         -AAGCTGAGCTGGCTAGGGAAAAAAC-AATGGGTACAAACTCGACAAGTC
genomic: GACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTC-AGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTC
EST: gi|149079566|gb|EE168554.2|EE168554
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|32828215|gb|CD967893.1|CD967893
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|31441047|gb|CD510478.1|CD510478
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|148971737|gb|EE022470.2|EE022470
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|32827850|gb|CD967528.1|CD967528
EST:     AGACATAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|60350764|gb|DN217737.1|DN217737
EST:     AAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
EST: gi|211181443|gb|FL114900.1|FL114900
EST:     AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAG                         GAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT
genomic: AGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCT

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), 49 (downstream exon)
Score: 555

CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCTCACATCTTTGCAGTCAATTTGCTCGATGATTTCGAGAAGTACATGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 477

CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCTCACATCTTTGCAGTCAATTTGCTCGATGATTTCGAGAAGTACATGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 443

CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCTCACATCTTTGCAGTCAATTTGCTCGATGATTTCGAGAAGTACATGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 408

CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttact ... tttttgccagGAAGCTGAGCTGGCTAGGGAAAAAACCAATGGGTACAAACTCGACAAGTCTCACATCTTTGCAGTCAATTTGCTCGATGATTTCGAGAAGTACATGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAATTGGAGCGATAAAAGAAAATGGTCTATGGATGCCTGTAAACCCAGAGACAAAGAAGACATACGGTTACTGTTTCATTGAGTATAGTACCCCTCAGgtattttacttgttggttgcgttttcttcttagttcttacctgcacaatgaagcaatgaacaatggcttaattatgttacctgttcaattcatccctcgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atccctcg