Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaggcatctggccaagattgtcatgcttaacctttttttttgtttcttgtttttgactcgtcaactatcctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 20
gtagaggcatctggccaagattgtcatgcttaac---------ctttttt------tttgtttcttgtttttgactcgtcaa---ctatcctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG
|||  | ||| || |||||| | || |  ||||          ||| ||       | | ||| || ||||    |  |||     ||| || | ||||| |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| |||
gtattgccatttg-ccaagactatcctatttaatagtacaatgcttattcagaaaatgtattttttattttatggtgatcacgttatattctctatacagTAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAG

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 11
gtagaggcatctggccaagattgtcatgcttaac---------ctttttt------tttgtttcttgtttttgactcgtcaa---ctatcctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG
|||  | ||| || |||||| | || |  ||||          ||| ||       | | ||| || ||||    |  |||     ||| || | ||||| |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| |||
gtattgccatttg-ccaagactatcctatttaatagtacaatgcttattcagaaaatatattttttattttatggtgatcacgttatattctctatacagTAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAG
















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|33093602|gb|CF053596.1|CF053596
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|211291669|gb|FL235609.1|FL235609
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|67014399|gb|CO443148.1|CO443148
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19822105|gb|BQ048129.1|BQ048129
EST:     AAGCTGGAAGAG-GTCTTCAA-TGCTAATAG-AAG                         CAATCGTATTCCGGATGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: AAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19822050|gb|BQ048074.1|BQ048074
EST:     AAAGCTGGAAGAGTGTCTTCAA-TGCTAATAGAAAG                         CAATCGTATTCCGGAAGCATGCATTGATGGCCAGATCTTATCTTCCTAGCA
genomic: AAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCA-GCATTGATGGCCAGATCTTATCTTCCTAGCA
EST: gi|26455841|gb|CA827424.1|CA827424
EST:     TCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19821970|gb|BQ047979.1|BQ047979
EST:     GAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: GAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|111145650|gb|EE257974.1|EE257974
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATNGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCCTAGCA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCC-TAGCA
EST: gi|19822070|gb|BQ048094.1|BQ048094
EST:     AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19822158|gb|BQ048182.1|BQ048182
EST:     AAGAGTGTCTTCAA-TGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: AAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|32929286|gb|CF034098.1|CF034098
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19821973|gb|BQ047982.1|BQ047982
EST:     AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGTAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCA
genomic: AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGG-AAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCA
EST: gi|32806736|gb|CD958970.1|CD958970
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATC
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATC
EST: gi|26456008|gb|CA827591.1|CA827591
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA

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), 47 (downstream exon)
Score: 342

TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 416

TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 501

TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 749

TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaacctttttttttgtttcttgtttttgactcgtcaactatcctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG
                          ttttgac  putative branch site (score: 749)
                                        ctatccttt  putative PPT
        tttttttttgtttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaggcatctggccaagattgtcatgcttaacctttttttttgtttcttgtttttgactcgtcaactatcctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG