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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaagcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttag

Basic information

species Zea mays
transcript GRMZM2G171354_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 5'ss of exon 7
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaagcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttag--
 ||||| ||||||||||||||||||||||||||||| || |||||  ||||||||||||||||||||||||| || || ||||| ||  ||||||||||||||||| |  | |    |  |    ||   |  |||| | ||  ||   | |||| || |||||||| |  ||| ||| |    
CCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATACATgtaagtctttatt----cttactacacttcaacttttgcatgggaaagatacttagtgcctaaggtaattatatatttcttcag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA14G07850.1 (Glycine max), 5'ss of exon 6
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaagcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttt-tag-------------------------------------------------------
  |||  | |||||||||  ||||||||||||| |||||   ||| || |||||||| ||||| || ||||||||||||||||||||  | |||||| ||||  ||  | | |        | |       |||| |  || | |   ||      | || |    ||  |||| ||||  ||                                                       
ATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACGGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAAATgtgcgtgccaatta---tttgatcttttattctttctgttttagagttttataggctttcaataaaataattatcttttacagtttacagagataatctgttggtatagtattgattgatacttcaatgttccattag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G01220.1 (Glycine max), 5'ss of exon 6
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggca-caagcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttag---------------
||| | ||||||||||||| | |||||||| || || ||  ||||  | ||||||||||| ||||| ||||| ||||||||||| ||  | ||||| |||||| || |  |      |  | ||| |   ||   | |  || || |   |     |   || |       | ||| || |                 
TCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTCATgtatgtataaataccctcttctagctatttaatgatctgtttaatgatggtttaagactgctgaaactgcttgatgcttctttggaaacattactcag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 6
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtt----tccactgaggcacaagcgacagaacttttttcttgataac--attgct-----taatgtctaaggtattctt----atgtt-tttag
||| | ||||||||||||  | |||||||| ||||| ||  || | |||||||||||||| ||||| || |||||||||||||| ||  | ||||| |||||| ||     | |  |   | |   |||  ||  || ||||| ||||     || |||      ||||  |   |  |  ||    || ||  ||||
TCTCTGCCAAATGTTTATCATAAATGCTGGACCGGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAAACAACTTCAAAGATTCATgtatgtaaaaatgctatattgtagctgcgttagg-ctcttttcatgatggtttatggctgctgacaatgcttggtgcctctttggaaatattgcttag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G03300.1 (Glycine max), 5'ss of exon 6
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgag-gcacaagcgacagaactttttt----cttgataacattgcttaatgtctaaggtattcttatgtttttag-------------------------------------------
 || | ||||||||||||  | ||||||||||| |||||   | | || |||||||| |||||  | ||||||||||||||||||||  | ||||| |||||| ||    | |    |  | || | |   | ||||       |  ||   | |  |||   ||||  || ||  | ||    ||                                            
ACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTCATgtatgtgataattttttgagctagtgtctatagttttaaaggattccattgaagtaattaccttctatagttttggtgtggagataatttataggtataggattaatgtacttgaatgttgttccattag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G37150.1 (Glycine max), 5'ss of exon 6
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaagcgacagaacttttt----tcttgataacat-----tgcttaat-gtctaaggtattcttatgtttttag-----------------------------------
  |||  | |||||||||  ||||||||||||| |||||   ||| || |||||||| ||||| || ||||||||||||||||||||  | |||||| ||||| || || | |     |   |     ||  ||| |    | |  || | ||     |||||    || ||  |   |  | ||||  ||                                    
ATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACAGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAAATgtatgtgtcaattatttgatctgtttttgatttttataggctttcaatgaaataatcatgcttttcagtttacagagataatctgttggtatagtattaattaattgatacttcaatgttccattag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G03230.1 (Glycine max), 5'ss of exon 5
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagt-----ttccactgaggcacaagcgacagaacttttttcttg-ataacattgcttaatgtctaaggtattcttatgtttttag---------------------------------------------
 || | ||||||||||||  | ||||||||||| |||||   | |||| |||||||| |||||  | ||||||||||||||||||||  | ||||| |||||| ||     ||    ||||  |      | ||   | |    ||  ||   | |  |||   ||||  || ||     |    ||                                              
ACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATACTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTCATgtatgtgttaatttttttgagttattgtttatagttttataggattccattgaagtaattaccttctatagttttggctcggagataatttataggtataggattaattgatacttgaatgttgtttcattag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaa----gcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttag--
|||  |||||||||||||| ||||||| || || || ||  ||||||| ||||||||||| |||  ||||||||| || || ||  | || || || |||||| |      || ||  | |          | |   || |  ||||| | || |  |    | |    ||||||  ||||| |    
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatctctatttaaaagtcttgtctttgattatatagaattcaatatggactattctattgtttatgtag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 7
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaagcgacagaacttttttcttgataacattgcttaatgtctaaggtattct-tatgtttttag--------------------------
||| | ||||||||||||| ||||||||||||| || ||  |||| || ||||||||||| ||| | ||||| ||||||||||| ||  ||||||| |||||  ||        | |          |  | || || ||| ||||  | |   |   |  ||  ||| || |||   |||                            
TCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTCATgtgcgt----gaaaatgtttttcttctatta-ttcttacttcataaattcgtagagccttcaaaatatgctgtataactttgtctctggggtttggaatttctcctcag

upper sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 5'ss of exon 6
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagttt-------ccactgaggcaca---agcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttag------------------------------------------
 || | ||||||||||||  | ||||||||||| |||||  |||| || |||||||| |||||| | ||||||||||| ||||| ||  ||||||| ||||||||||          | |           || |   || ||   |  ||| ||  | ||   | |||     || ||||| |  || ||                                           
ACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTCATgtaagttaaaagaagttattttaatctgtttagagtatgatctccctgtttgttagaagtgtacactgtgct--gttttctt-tacttctaacagaagtcataaggagtgattgtttttggaaattttcctcag

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|71447517|gb|DR828567.1|DR828567
EST:     GTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
genomic: GTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG




















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: 208

TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG