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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtattgcctattgatactattgcatggctctatacatgattcagttacttatatgtgttgccacctaatctgaaaattcctctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG

Basic information

species Zea mays
transcript GRMZM5G824405_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
gtcagtattgcctat-tgatactattgcatg--gctcta---tacatgattcagttacttatatgtgttgcc-----acctaatctgaaaattcctctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG
|| | |   | |||| ||| | |||  ||||  |   ||   ||| | |||||  || || ||  | ||  |     || | ||||  | | || ||| ||| |||| |||||||||| || ||||| |||||||| ||||||||||||||||| |||||| ||||||||
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcaccta-ttgtaactattatcggtgcactttatctttacagtcttctctgttcagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG
















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|78022287|gb|DV490674.1|DV490674
EST:     CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
genomic: CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
EST: gi|5714261|gb|AI944246.1|AI944246
EST:     CCGAAAGGAGAATCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGATAATTGAACTTGAACGACAAGCGTGCTCCAGTTGTAG
genomic: CCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGAC-AGCGTGCTCCAGTTGTAG
EST: gi|211455219|gb|FL443686.1|FL443686
EST:     CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
genomic: CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
EST: gi|78021450|gb|DV489837.1|DV489837
EST:     CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
genomic: CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
EST: gi|5714269|gb|AI944254.1|AI944254
EST:     CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
genomic: CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
EST: gi|67015674|gb|CO444423.1|CO444423
EST:     CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
genomic: CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGT
EST: gi|67010650|gb|CO439399.1|CO439399
EST:     CTGAGGTATCGTTATCCGAGAAGAGA-TCCTATCTTGACGTCATTCAAAG                         ACTAGAACCTGTGNATA-TTGAACTTGA-CGACAGCGTGCTCCAGTTGTAG
genomic: CTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTG-ATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAG

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: 97

ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 124

ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 121

ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAGgtcagtattg ... ctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcagttacttatatgtgttgccacctaatctgaaaattcctctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG
                          acctaat  putative branch site (score: 311)
                                        ttcctctat  putative PPT
        ttacttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtattgcctattgatactattgcatggctctatacatgattcagttacttatatgtgttgccacctaatctgaaaattcctctatgtccagACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA