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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacatttctttcaccacctgattattagtacccccagcgagactgatgagagtgaggaattgaacgactgatggatcgcgtccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG

Basic information

species Zea mays
transcript GRMZM2G140201_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140201_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g54300.1 (Oryza sativa), 3'ss of exon 4
gtaaacatttctttcaccacctgattattagtaccccca----gcgagactgat-gagagtgaggaatt---gaacgactga---tggatcgcgtccgcgcgcagGCTGCTG-CAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG------
|||| ||        |||| |  | ||  |||| || ||    | ||  || |   | ||  || |||    |||  | |||   |  ||   |     |  | |   || |   |||||||||||   |||||||||||||||||||| ||| ||||||| |  |  ||||| | |||||||| |||  ||||||||  |||||       
gtaaccaaccaaccaaccaaccaactag-agtatccacaaatggagaagctaaccaatagccagaaatgggggaaacattgaagcttaatttggatgatgaactgatcgcagGTTGCAGCACGCCAGTCTGGACGAGAAGCTCAAGTTCATGACGCGGTGGATCACCGCCCACGTGGAGGACGGCGACGGGGAGCTGGAGAAGCCCGTGCTG
















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|71320023|gb|DR796776.1|DR796776
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|76925654|gb|DV170534.1|DV170534
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|91872767|gb|EB402724.1|EB402724
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|26559897|gb|CA832132.1|CA832132
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|94475116|gb|EB704074.1|EB704074
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|71759123|gb|DR957060.1|DR957060
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|6859995|gb|AW355989.1|AW355989
EST:     CCCANACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: CCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|22819005|gb|BU499095.1|BU499095
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|74236575|gb|DT644489.1|DT644489
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|101402159|gb|EB822679.1|EB822679
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|71429197|gb|DR810247.1|DR810247
EST:     AAGATCCCAGACTTGGATTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GGTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|76925539|gb|DV170474.1|DV170474
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|76011546|gb|DT938716.1|DT938716
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|211476410|gb|FL048979.1|FL048979
EST:     ATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GSTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: ATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|78080284|gb|DV508696.1|DV508696
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|78179880|gb|DV550253.1|DV550253
EST:     GACATCGACTTCGCTTCC-TCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: GACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|71763540|gb|DR961477.1|DR961477
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|12045849|gb|BF728092.1|BF728092
EST:     CCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: CCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|148943312|gb|EC888372.2|EC888372
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|78122934|gb|DV541318.1|DV541318
EST:     CCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: CCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|71426841|gb|DR807891.1|DR807891
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|101392224|gb|EB818040.1|EB818040
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|87155942|gb|DY400731.1|DY400731
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|84969778|gb|DW468202.1|DW468202
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|148941701|gb|EC886652.2|EC886652
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
EST: gi|78092980|gb|DV521354.1|DV521354
EST:     AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTG                         GCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG
genomic: AAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCG

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 23

CGGGCACGTGGAAGGACAACAACTACGGTTCGGACTTCATCCGCAACGCCAAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG


Block sizes: 20 (upstream exon), 30 (downstream exon)
Score: 1

CGGGCACGTGGAAGGACAACAACTACGGTTCGGACTTCATCCGCAACGCCAAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG


Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 5

CGGGCACGTGGAAGGACAACAACTACGGTTCGGACTTCATCCGCAACGCCAAGATCCCAGACATCGACTTCGCTTCCATCCACCTCTACCCTGACACCTGgtaaacattt ... ccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgagactgatgagagtgaggaattgaacgactgatggatcgcgtccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG
                             gactgat  putative branch site (score: 5)
                     aattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacatttctttcaccacctgattattagtacccccagcgagactgatgagagtgaggaattgaacgactgatggatcgcgtccgcgcgcagGCTGCTGCAGCAGCACGCCACGGTGGACGAGAAGCTCAAGTTCGTGAAGCGGTGGGTGGCGTCCCACATCGAGGACGGGGACAAGGAGCTGGGCAAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT