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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaacttgtactttcatactggatggttcctttttgttagcataaagtctacttggaaaatgtagtctactcaattctaatacacttccactggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 10
---gtaactt-gtactttcatactggatggttcctttttgttagcataaagtcta---cttggaaaatgtagtctactcaattctaatacacttccactggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC
    | | |  | |  | ||||      |  || |||||    |  |||||| ||    |||||| ||  | | ||     | || ||| ||||| | | |||||||||||||||||| |||||||| || |||||||||||| ||||||||||||||||| |||| ||||||||||||||| |||| || ||||||||||||||||
tttatgattgaggaagtccatat--accgcatctttttttgacgtgtaaagtgtaatgtttggaatattcaattta-----tgctgatatacttctaattgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGTGGACCACAGCTTCTCTTTCTGGACCTGTGCTCTGCCTTTCTAACTCAGC
















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|31351266|gb|CD435623.1|CD435623
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|37378483|gb|CF625932.1|CF625932
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|76933414|gb|DV173440.1|DV173440
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|76934829|gb|DV174039.1|DV174039
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|60344416|gb|DN211389.1|DN211389
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|89763299|gb|DY690559.1|DY690559
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|211090138|gb|FL283400.1|FL283400
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|5713666|gb|AI943658.1|AI943658
EST:     CTGATGTTTTCATGGAGAAATCACCCCCGCCAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|91878197|gb|EB408154.1|EB408154
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|78075975|gb|DV504409.1|DV504409
EST:     GGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: GGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|213175124|gb|FM193003.1|FM193003
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|76934830|gb|DV174040.1|DV174040
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|76933421|gb|DV173441.1|DV173441
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|67028292|gb|CO457041.1|CO457041
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|40334512|gb|CK368582.1|CK368582
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|76012619|gb|DT939789.1|DT939789
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|32835075|gb|CD974753.1|CD974753
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAGACGAGGGATGAGAAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGT
EST: gi|37376193|gb|CF624601.1|CF624601
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|211090139|gb|FL283401.1|FL283401
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTYTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|40303812|gb|CK348199.1|CK348199
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|78108755|gb|DV527172.1|DV527172
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|60395300|gb|DN228169.1|DN228169
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|78027099|gb|DV495486.1|DV495486
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
EST: gi|37380652|gb|CF627152.1|CF627152
EST:     CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAG                         CTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT
genomic: CTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGT

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: 45 (upstream exon), 49 (downstream exon)
Score: 225

TATGATGCATAACAGTGATAGCTTCAGTGCGGAGTCTGCTATAATTGAAACTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TATGATGCATAACAGTGATAGCTTCAGTGCGGAGTCTGCTATAATTGAAACTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

TATGATGCATAACAGTGATAGCTTCAGTGCGGAGTCTGCTATAATTGAAACTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

TATGATGCATAACAGTGATAGCTTCAGTGCGGAGTCTGCTATAATTGAAACTGATGTTTTCATGGAGAAATCAACCCCGACAGTGAAGTTTGAGATTCAGgtatcattcg ... ctggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctacttggaaaatgtagtctactcaattctaatacacttccactggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC
                             ttctaat  putative branch site (score: 147)
                                       cttccact  putative PPT
                           aattctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgtactttcatactggatggttcctttttgttagcataaagtctacttggaaaatgtagtctactcaattctaatacacttccactggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC

- - - - - ctttcat
- - - - - - - - - ctggatg
- - - - - - - - - - - - - - - -ttttgtt