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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaacatgcctttttgtctatatggttcaatcttagtcctttacattactgataaatgtctatttatcatgaaag

Basic information

species Zea mays
transcript GRMZM2G065494_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065494_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 9
GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaacatgcctttttgtctatatggtt----caatc------ttagtcctttacattactgataaatgtctatttatcatgaaag
||| |||||||||| ||||||||| || ||||||||   ||| |  ||||| |||||||| || ||||||||||||||   ||| || |||||| | ||||| ||  |  ||||| | ||    |||| | ||     ||||      | |  || |  ||||||| |    || || |||||| ||||||
GGACACAGCTTTCACAGTTCAAGCTATAGTGGCTACTGGCCTCATTGAAGAATTTGGTCCTACTCTTAAACTAGCACATGGCTACATAAAGAAAACGCAGgtgcatgcctcatgcatgttcccttatacgattatactaatcaacatttcaagccatctcattacttacctgtggct-tttatcctgaaag
















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|28909848|gb|CB331129.1|CB331129
EST:     AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAG                         GTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
EST: gi|31356628|gb|CD440985.1|CD440985
EST:     AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAG                         GTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
EST: gi|22489164|gb|BU049087.1|BU049087
EST:     AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAG                         GTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
EST: gi|18383894|gb|BM417094.1|BM417094
EST:     AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAG                         GTTCTTGACGACTGCCCTGG-GATCTGAATGACTGGTACCGTCACACATCT
genomic: AGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT

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: 129

GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGCGCATGGCCATTCTCCACCGCGGATCATGGTTGGCCTATATCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 144

GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGCGCATGGCCATTCTCCACCGCGGATCATGGTTGGCCTATATCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 63

GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGCGCATGGCCATTCTCCACCGCGGATCATGGTTGGCCTATATCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaa ... atcatgaaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGCGCATGGCCATTCTCCACCGCGGATCATGGTTGGCCTATATCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACAGCTTTCATAGTTCAAGCCATTGTGGCTACCAACCTTACCGAAGAGTTTGGTCCCACCCTTAAACTAGCACACAACTATATCAAGAAATCACAGgtacagtcaacatgcctttttgtctatatggttcaatcttagtcctttacattactgataaatgtctatttatcatgaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA