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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcaattatcctgtccaacagttatgatttgcattagcttgttagttactattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g58580.2 (Oryza sativa), 3'ss of exon 6
gtcagtcaattatcctgtccaacagttatgatttgcattagcttgttagttactattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG
|||||| ||  | ||| || |  |      |||  |||| |        |   ||| ||||        | |  ||| ||  ||||||||||||||||||||||||||||||||||| | ||||| || || ||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| ||||||
gtcagtgaacaaacctatctacta------attcccattgggcaacagctccttatggacca-------aataactgtttcatcagGGGTACATTCATAGAGTTCCGAAGTGGAATGCTGAATGTGTCGCCCATAGGGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 7
----------gtcagtcaattatcctgtccaacagttatgatttgcattagc-ttgttagttactattgaccttca--taatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG
           |      ||||   | |  |    ||  ||||||   ||   || |  |  ||| |||      |  | ||||    |  ||  | ||||| ||||| ||||||||||| ||||| ||| | ||||| || ||||| ||  |||| ||||||||||||||| | ||||| |||||||| || || || 
ggttagtgggattcagagattaatatatatatatttttagatttgttataatgttatatgaaactgttggttactaattgatataaaatattt--ttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA-

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 7
-----------------gtcagtcaattatcctgtccaa--cagttatgat-ttgcattagcttgttagttactattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG
                 || | | | || |  | || |     |||||||| ||  || |   |||| ||||||| |     | | ||||||          | ||||| ||||| || |||||||| ||||| ||| | ||||| || ||||| ||  |||||||||||||||||||| | ||||| |||||||| || || |||
gttagtgggattcagaggttaat-attttttttttctagatttgttatgatgttatatgaaactgttggttactaattgatataacaatatt---------tttagGGGAACATTTATGGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 7
lower sequence: AT2G45790.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagtcaattatcctgtccaacagttatgatttgcattagcttgttagtta--ctattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG
||    |    ||||   |    |||    | |    || ||    |  | |    ||| |  ||| | | |||   ||  | |  ||||| ||||| || || ||||||| ||||||| | |||||||| || || ||  | ||||| |||||||||||| | |||||||||||||  || ||||||
gtataacgtggatccaa-ctgctagtctctaatcatgtttgcaaagtgataagatgatttattttcttgaaatt---tgtatacatagGGGAACATTTATTGAATTCCGAAATGGAATGCTCAATGTATCACCCATTGGTCGCAACTGCAGCCAAGAAGAAAGAGATGAATTTGAGAGATATGATAAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 6
gtcagtcaattat---cctgtccaacagttat-gatttgcattagcttgttagttactattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG
|| ||  ||  |    ||||   | |||||||  |||| ||||   | | | | |||  |   |  || |||| |       ||  ||||||| || || ||||||||||||||||| ||| | |||||||| || || ||  ||||||| ||||| ||||| || ||||| ||||| ||||| || |||
gttagcaaagcagaaacctgaatagcagttattaatttacatt---tagattgatacgttc--ctctcttaatttc------ttcttcagGGGAACCTTTATAGAGTTCCGAAGTGGGATGCTCAATGTATCACCAATTGGGCGAAACTGCAGCCAGGAAGAGCGTGATGAGTTTGAAAAGTATGACAAG

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|6020771|gb|AW065579.1|AW065579
EST:     NTTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: -TTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     TCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: TCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     ATTAACTTCACTCTTCATTATATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|32919710|gb|CF024522.1|CF024522
EST:     ATTAACTTCACTCTTCATTATATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|148950412|gb|EC895979.2|EC895979
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|14646044|gb|BI180233.1|BI180233
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|6056459|gb|AW090849.1|AW090849
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     TCATTCCATTGCTGACTTGGATATCCCAATTAAAAG                         GGGGACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: TCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG                         GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG
genomic: ATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGG

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: 36 (upstream exon), 49 (downstream exon)
Score: 144

GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 396

GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 289

GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 397

GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAGgtcagtcaat ... gattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcattagcttgttagttactattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG
                              ttcataatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtcaattatcctgtccaacagttatgatttgcattagcttgttagttactattgaccttcataatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT