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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttccaagttgctggcaacaatctcctcacgaattatgtttatctgtaccttataaatttcacgtgaacag

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 9
CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagttt-ccaagttgc-tggcaacaatctc-ctcacgaattatgtttatctgtaccttataaatttcacgtgaacag
||| || || |||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||  |||| |||||||||||||||||||||||||  |||    |||||   |||||  | ||   ||| || | ||||| ||   | | |   ||| || || ||  |||
CCACGGTTCGGTTGGAGCTGTTGCAGGTCGCCGTGCTATAGCTCAAGGAAACCCTGATGAAGTTGCTGCAGCGCTGTGCAGATATTCAGCACCAGAAGAGgtatgctttattcagttgtacggcaattaccttattcaagactaatgttcattcatgcttacaaaaatttacttggtcag
















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|211367141|gb|FL432366.1|FL432366
EST:     ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|30306974|gb|CD001647.1|CD001647
EST:     TGAAG-TGCTGCAGCA-TG-GTAGATATTCAGCACCAGAAGAG                         G-TGATACTTTACCATCAACATGTGGAGCCTG-GG-ACAGAATGCGTCACA
genomic: TGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|78085694|gb|DV514087.1|DV514087
EST:     ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|31611962|gb|CD568584.1|CD568584
EST:     ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|67020485|gb|CO449234.1|CO449234
EST:     ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|29946582|gb|CB816222.1|CB816222
EST:     ACCCTGATGAAGTTGCTGCAGCATTG-GTAGATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATG-GGAGCCTG-GGAACAGAATGCGTCACA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|28568977|gb|CB280852.1|CB280852
EST:     ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|211367140|gb|FL432365.1|FL432365
EST:     ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCMCCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCMCA
genomic: ACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
EST: gi|60357973|gb|DN224946.1|DN224946
EST:     GATATTCAGCACCAGAAGAG                         GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA
genomic: GATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACA

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: 182

CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttc ... acgtgaacagGTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGGCTCAGTTGGAGCTGTTGCAGGTCGTCGTGCTATAGCTCAGGGAAACCCTGATGAAGTTGCTGCAGCATTGTGTAGATATTCAGCACCAGAAGAGgtatagtttccaagttgctggcaacaatctcctcacgaattatgtttatctgtaccttataaatttcacgtgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG