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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaatttaaatgttttacttgctttcttagtgtgtatcttcttatcctcctcgtag

Basic information

species Zea mays
transcript GRMZM2G178546_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGG------CGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaatttaaatgttttacttgctt-----tcttagtgtgtatcttcttatcctcctcgtag
   ||| ||||||||||| ||||||||||| || ||||| |||||||||||| ||   || || | |||       |||||||||||  |||| ||||||    | ||| |||  |||| | ||| ||| ||    |   |||| | |  ||||        |  || |  ||   | ||| |    ||| |||
---GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCT---GATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagctttgttgattttttccacagac--aaatttctctcttgtgacaaaattctaattagttattgctt-tttggctcatag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G36570.1 (Glycine max), 5'ss of exon 5
ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaatttaaatgttttacttgctttcttagtgtgtatcttctt--atcctcctcgtag-------------------------------
| | || |||||||| || |||||||||||||| || |||||||||||  |  ||         |||  | |  | || ||| |||| || ||   ||| ||  |   | ||   |  | | || |  |||| |   | | | | |  || ||| | | | | |  ||||  ||  |     ||                                
ACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAAATTGCATTAGGTCTACAGACAAGCAGgtacagggagttga-aagtttctatctgcaatctgt-tttgtgaatatctctctcactttctgttctcttgaattatttcattaaatggcttctgttattatctttaaatttacag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 5'ss of exon 4
ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaatttaaatgttt-tacttgctttcttagt-gtgtatcttcttatcctcctcgtag----------------------------------------
  | ||||||||||| || ||||| |||||||| ||||||||||| ||  |  | | |       |        | |||||| ||| ||||||   ||| || |  |||   |  | |   || | |   |  || || | | ||  | || |||   |  | | |  | ||||     | ||                                          
GCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAAATTGTATTAGGTTAACTGACAAGCAGgt-accctagcctagaaactctttctcatgaaatatatatatatatatactatctctttcatatgttatgttatttatttggttttacttattcacccttttatattattttcttatgaatgtag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S47_110V6.1 (Physcomitrella patens), 5'ss of exon 5
---ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaact--actttctagatctt--taccctcaatttaaatgttttacttgctttcttagtgtgtatcttcttatcctcctcgtag-----------------------------------------------------------------
    |||||||| |||||||| ||||||||||| |||||||| ||||  |  |   | | ||  |  || | |   | |   | |||    |  ||   | | |||    |  | |||| || | ||  ||   | || | ||| || ||| ||  |||  | || | | |||  || |   |     |                                                                  
GGAGTTGTACTATGCTGGAAGTCATGGAATGGATATAATGGGTCCTGCAAAAAGTTCAAGTGGTTTTAAAGTCAACGGA---ACTCGAGTTAAAGACAAGAAGgtggtttttaattttcaagtttttgataattttaactcaaa-gtcttaattttttttattgtttctctctgtttgtaaactaatgaacatatatgtcgctagtaggttattcgaatcgtccgctccttctaacaatgattgttactgttcag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S141_116V6.1 (Physcomitrella patens), 5'ss of exon 4
---ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaa-------tttaaatgttttacttgctttcttagtgtgtatc-ttcttatcctcctcgtag-------------------------------------
   |||||||||||| ||||| ||||||||||| |||||||| ||||  |  |   | | ||  |  || | |   | |   | |||    |  ||   | | ||||      |  || ||  | |||   |||       | | |      ||| ||    ||  || | | || ||| ||  ||  |  ||                                      
GGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACGGA---ACTCGAGTTAAAGACAAGAAGgtgagttccatgacttgacttatactgccaagttcatatctgagaccgatacatgacacctgtgtatatgtccttcgtaagcttattttaattgtctactcctgcttacaaagattttctttgcacag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S201_97V6.1 (Physcomitrella patens), 5'ss of exon 4
---ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAA------TGGCGT-------------------GGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatcttt---accctc----aatttaaatgttttacttgctttcttagtgtgta---tcttcttatcctcctcgtag------------------------------------------------
    |||||||| || ||||| |||||||||||||||||||| ||||  |  |   | | ||  | |||      ||||                     |  || | |||  |||||  |  |   |     ||  ||| ||||  |||    | | |     |||||  |  ||||| ||  | |||| |     |    |||||||   |    |||                                                 
CGAGTTGTACTATGCGGGAAGTCATGGAATGGACATAATGGGTCCTGCAAATAGCGCAAGTGTTTTCAAGATCAATGGCACTCTAGCGAAAGACAAAATGgtgatcttttctttcaacctacataactccaggacc-cttactagcgcttgttgagcattgaagaatttttacattttattttttctcttcgaaaacaaatccttcttaatatagctgtaagctcacccaatccttctgctcctactcacataacgtttcgttaaacag

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|31349982|gb|CD434339.1|CD434339
EST:     AGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCAT                         GGTAAAGAAGTCAACCTGTTCCAACCTGCTAGTGAGTTTTTACCTATGATC
genomic: AGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactac ... ctcctcgtagGGTAAAGAAGTCAACCTGTTCCAACCTGCTAGTGAGTTTTTACCTATGATC




















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: 47 (upstream exon), 48 (downstream exon)
Score: 78

ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactac ... ctcctcgtagGGTAAAGAAGTCAACCTGTTCCAACCTGCTAGTGAGTTTTTACCTATGATCACTGAG


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 31

ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactac ... ctcctcgtagGGTAAAGAAGTCAACCTGTTCCAACCTGCTAGTGAGTTTTTACCTATGATCACTGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 34

ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactac ... ctcctcgtagGGTAAAGAAGTCAACCTGTTCCAACCTGCTAGTGAGTTTTTACCTATGATCACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactac ... ctcctcgtagGGTAAAGAAGTCAACCTGTTCCAACCTGCTAGTGAGTTTTTACCTATGATCACTGAG