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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggccaagtttcgattacattctttgttctttgttgtttttgtatccacatacctattttgtttctgattccttcctatctctcaataacaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC

Basic information

species Zea mays
transcript GRMZM2G066362_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g07720.4 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------tgtggccaagtttcgattacattct---ttgttctttgttgtttttgtatcca---catacctatt-ttgtttctgattccttcctatctctcaataacaat-gacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC
                                                                                  | ||  | |    ||     ||| |   ||||  |        |   |  |       | |||| | || |||||||  ||| ||| | |  | ||||   | ||||||||||| |||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| |||||||| || || ||||| ||||| || ||||
gtagggatgcctgtgttctctcctggtttgctcttagtttagcaatactcatctgatcactttgctagttcaagcaggacaatttgatcgaaccgcggaactattttgggttgtattaaacatcctccatgactgatgtgtgcctaatgttatttctgaa-cctccctgtttacccataatttttgacagCTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAAGAGGGTTCACTCCATCTTTGTGCTCCGCCTTTTCAACGATTGTTTCGCTATGACGTTTCTCC

upper sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G47760.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------------------tgtggccaagtttcgattacattctttgttctttgttgtttttgtatcca--catacctattttgtttctgattccttcctatctctcaataacaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC
                                                                           |||     |       ||   || |   || | ||||  |  ||          ||   | ||   |  ||||  ||     | | ||  ||   ||  ||| | ||||||||||| ||| || | || ||||| ||||||||| | || || ||||||||||||||||| || ||||| || || ||||||||  | || |
gtataaatgaagacttatttcttatctcttttcatcaagtatttgtagacgttgtcaagcgttgtccatttacgatgttaatgaacaatattttggttttgatttgtctgtttatgatgggagtgattttagtgaattcagtgatgatatctcttcttgtatccttacgtatttcagGTGCCATGGTGGGCATTAAGTCTACTATGTTTATCCAAGAGGATACATTCAATCTTTGTTCTCCGTCTCTTTAATGATTGTTTTGCCATGACTCTCCTAC

upper sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G47760.2 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------------------tgtggccaagtttcgattacattctttgttctttgttgtttttgtatcca--catacctattttgtttctgattccttcctatctctcaataacaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC
                                                                              |||     |       ||   || |   || | ||||  |  ||          ||   | ||   |  ||||  ||     | | ||  ||   ||  ||| | ||||||||||| ||| || | || ||||| ||||||||| | || || ||||||||||||||||| || ||||| || || ||||||||  | || |
gtggtataaatgaagacttatttcttatctcttttcatcaagtatttgtagacgttgtcaagcgttgtccatttacgatgttaatgaacaatattttggttttgatttgtctgtttatgatgggagtgattttagtgaattcagtgatgatatctcttcttgtatccttacgtatttcagGTGCCATGGTGGGCATTAAGTCTACTATGTTTATCCAAGAGGATACATTCAATCTTTGTTCTCCGTCTCTTTAATGATTGTTTTGCCATGACTCTCCTAC

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|71446401|gb|DR827451.1|DR827451
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|149090152|gb|EE179452.2|EE179452
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|71768739|gb|DR966676.1|DR966676
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|78103804|gb|DV522232.1|DV522232
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|76929771|gb|DV172155.1|DV172155
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|76917523|gb|DV166878.1|DV166878
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|148950403|gb|EC895970.2|EC895970
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|71438024|gb|DR819074.1|DR819074
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|50327840|gb|CO522966.1|CO522966
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|149008598|gb|EE040780.2|EE040780
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|213188075|gb|FM194957.1|FM194957
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|101394910|gb|EB819389.1|EB819389
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|93014216|gb|EB639736.1|EB639736
EST:     CATTGTCAACTTGAGCCTCACCTCTTCTGCTTTACGTCCAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: CATTGTCAACTTGAGCCTCAC-TCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
EST: gi|149078217|gb|EE166971.2|EE166971
EST:     ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC
genomic: ACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCC

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), 48 (downstream exon)
Score: 46

ATTTTGTTTGGCGTCTTGTACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 53

ATTTTGTTTGGCGTCTTGTACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

ATTTTGTTTGGCGTCTTGTACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 74

ATTTTGTTTGGCGTCTTGTACATTGTCAACTTGAGCCTCACTCTTCTGCTTTACGTCAAGACTGAAGTGgtatatagtt ... acaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccacatacctattttgtttctgattccttcctatctctcaataacaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC
                                        caataac  putative branch site (score: 74)
           tattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggccaagtttcgattacattctttgttctttgttgtttttgtatccacatacctattttgtttctgattccttcctatctctcaataacaatgacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC

- - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - cacatac