Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgggatctgttcctgtcggttatcagaagaatctaatcatgtttaatgcatgttaaggttgtgcatcagaatgctcactgttgtacctcccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG

Basic information

species Zea mays
transcript GRMZM2G078839_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078839_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g12260.1 (Oryza sativa), 3'ss of exon 4
--tgtgggatctgttcctgtcggttatcagaagaatctaatcatgtttaatgcatgttaaggttgtgcatcagaatgctcactgttgtacctcccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG
   |    | |  ||  | |    ||  |    |    ||||||||||| |  ||| |||   | |  ||| ||||||    | ||     |    || |||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||| ||||||||||| |  |||| ||||||||||||||||| ||||||
gaagctatagccatttttctta--tactaatcaaccaaaatcatgtttattagatgataactatatagatctgaatgcctgatatttgtaatttttatttagCTCTGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATAGTCTGTGAAAATACATTGGATGCTAGACTAGAGGTGGTTTTCAGAAAGAAGCTACCAGAG

upper sequence: GRMZM2G078839_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G02390.2 (Glycine max), 3'ss of exon 4
tgtgggatctgttcctgtcggttatcagaagaatctaatcatgtttaatgc----atgttaaggttgtgcatcagaatgctcactgttgtacctcccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG
    |  ||   || ||  | |||  | ||  || | | | | || | |||    || | ||  ||  |    || |  |    | || |   |    ||  ||||| ||||| || ||| | ||||| || |||||||||||||| |||||||| ||||| |||||  |  |  | ||||||||| | || ||||| ||||||
--cagtttcaaatcttga-gattaataaaatcatattagc-ttttaactgctttgatatcaaatttcagttgtagcacacctgattttttttgttgatattcagCTCTGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGTGAAAATACACTTGATGCACGTCTTGATGTAGTTTTCCGTAAAAAGCTTCCAGAG

upper sequence: GRMZM2G078839_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G37190.1 (Glycine max), 3'ss of exon 4
tgtgggatctgttcctgtcggttatcagaagaatctaatcatgtttaa-tgcatgttaaggttgtgcatcagaatgctcactgttgtacctcccaatgt--agCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG
 |    ||||| |   |   | | ||  || |   || |    ||||  ||| |  | |  ||     |   ||  | |    || |   |    || |  ||||||||||| || ||| | ||||| || |||||||||||||| |||||||| || || |||||  |  |  | ||||||||| | || ||||| ||||||
-gattaatctgattgaggatgct-tcctaaaatcatattagcttttagctgctttgtcaaatttca-gttgtaacacacctgattatttttgttgatattcagCTCCGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGTGAAAATACTCTTGATGCACGTCTTGATGTAGTTTTCCGTAAAAAGCTTCCAGAG

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|37401003|gb|CF637863.1|CF637863
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGTCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|91051896|gb|EB162314.1|EB162314
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCGGGTGGAGTTGTGCTAGCTTCCCGAGAT
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGAT
EST: gi|32932813|gb|CF037625.1|CF037625
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGTCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|211317448|gb|FL406235.1|FL406235
EST:     ATCTATCTGGCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CCCCCGGTGGAGTTGTGGCTAGCT-CCCGAGA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCC-GGTGGAGTTGTG-CTAGCTTCCCGAGA
EST: gi|37379237|gb|CF626354.1|CF626354
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGTCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|149106149|gb|EE291827.2|EE291827
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|29946371|gb|CB816117.1|CB816117
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|71431176|gb|DR812226.1|DR812226
EST:     CTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: CTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|71443317|gb|DR824367.1|DR824367
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|76016568|gb|DT943738.1|DT943738
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|211030346|gb|FL424791.1|FL424791
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGTCTCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|71431175|gb|DR812225.1|DR812225
EST:     TGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: TGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|16916530|gb|BM072882.1|BM072882
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|16927534|gb|BM080603.1|BM080603
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|31911224|gb|CD651817.1|CD651817
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|74234972|gb|DT642886.1|DT642886
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|94479251|gb|EB708209.1|EB708209
EST:     ATCTATTTGCCATTTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTTTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|15426825|gb|BI542647.1|BI542647
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|71443402|gb|DR824452.1|DR824452
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|29946284|gb|CB816072.1|CB816072
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
EST: gi|4388055|gb|AI491227.1|AI491227
EST:     ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATG                         CTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA
genomic: ATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAA

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), 47 (downstream exon)
Score: 107

ATGCAGATAAAGCAAAAGTATATCCTCCTGAGATAGTGGTAGATCGTCAAATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 189

ATGCAGATAAAGCAAAAGTATATCCTCCTGAGATAGTGGTAGATCGTCAAATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

ATGCAGATAAAGCAAAAGTATATCCTCCTGAGATAGTGGTAGATCGTCAAATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

ATGCAGATAAAGCAAAAGTATATCCTCCTGAGATAGTGGTAGATCGTCAAATCTATCTGCCATCTGCTCCCAGTCATTATCAGGCACCTGGCCCCTCATGgtaaggcttg ... cccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgcatgttaaggttgtgcatcagaatgctcactgttgtacctcccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG
                            tgctcac  putative branch site (score: 153)
                                        tacctccc  putative PPT
      atgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgggatctgttcctgtcggttatcagaagaatctaatcatgtttaatgcatgttaaggttgtgcatcagaatgctcactgttgtacctcccaatgtagCTCCGGTGGAGTTGTGCTAGCTTCCCGAGATGGAAAGATTGTCTGTGAAAACACACTGGATGCTAGATTGCAGGTAGTTTTCAGAAAGAAGCTGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - gttcctg
- - - - - - - - - - - - -cagaagaa
- - - - - - - - - - - - - - - - - - - -catgttt
- - - - - - - - - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt