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

gtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA

Basic information

species Zea mays
transcript GRMZM2G047143_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047143_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g40940.2 (Oryza sativa), 3'ss of exon 3
gtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggt----cagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA
||||| |||   |||  || |    |   | | || ||      |             |  | |  |||   || | |   || |||     | |  | |  |  |    |     | || |    ||||| | |||||||||||||| ||||| |||| ||||||||  |  ||   ||||||||| ||||| ||||||||||||||||| || || |||||||| ||
gtaagcgccattaccaccacctctacttcttcagtgttcagtgttcatcgcctctgctctcccccccaattcctcccagctcatccgcattcgtcgattgattgattgattgattgattgattttgcagGCATATTCGACGTGCTGGCGTACACCGACATGGACGTCGCGGTGCCCTTCACCTGGGTGGAGAGCGACGCCAAGCTCATCGAGAATCCACAGATGGTGAA
















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|31406271|gb|CD485003.1|CD485003
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|76019513|gb|DT946683.1|DT946683
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTTGACGTGCTGGCCTACACGGACACGGACGTTGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|34391357|gb|CF384585.1|CF384585
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32800674|gb|CD952910.1|CD952910
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32797390|gb|CD949626.1|CD949626
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32790500|gb|CD942736.1|CD942736
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGGGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|101396573|gb|EB820212.1|EB820212
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32797842|gb|CD950078.1|CD950078
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|31997662|gb|CD661703.1|CD661703
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|211015021|gb|FL312920.1|FL312920
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|91054081|gb|EB164499.1|EB164499
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTTGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|87155980|gb|DY400769.1|DY400769
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|31441067|gb|CD510498.1|CD510498
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|101396571|gb|EB820211.1|EB820211
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTGGACGTGCTGGCCTACACGGACACGGACGTGGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|91054064|gb|EB164482.1|EB164482
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTTGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|31664270|gb|CD572995.1|CD572995
EST:     GTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|211437588|gb|FL436643.1|FL436643
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|148946894|gb|EC892174.2|EC892174
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|78078551|gb|DV506963.1|DV506963
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTTGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|5713718|gb|AI943710.1|AI943710
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|60349178|gb|DN216151.1|DN216151
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|94475186|gb|EB704144.1|EB704144
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|78023687|gb|DV492074.1|DV492074
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32797599|gb|CD949835.1|CD949835
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|12969132|gb|BG266077.1|BG266077
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGGCGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|4966592|gb|AI691448.1|AI691448
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32912163|gb|CF016975.1|CF016975
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA

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: 146

ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 8

ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA


Block sizes: 38 (upstream exon), 42 (downstream exon)
Score: 11

ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 17

ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA
                  ggctgac  putative branch site (score: 17)
                              tctcctctcctcccga  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG