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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggatacacaaacacaaatgcataatcttttccatagctcttgcaagatgtttctttcagaaatctagagccaataattgtacgtccattttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG

Basic information

species Zea mays
transcript GRMZM2G037431_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 1
aggatacacaaacacaaat-gcataatcttttccatagctcttgcaagatgtttctttcagaaatctagagccaat--aattgtacgtccattttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG
 |  |       || |  | ||||| |    || | ||  |   || ||   |   |||| | ||| |      |   || |||   |        ||| ||||| ||| ||| ||| |||||||| || ||||  ||||| ||||||||| || |||||||| ||||||| ||||| ||||||||||||||||| |||||||
-gtttctgggttcatatttagcatactacagtctagaggac--acaggacagtggcttcaaatatcaaagtttgagcaaaatgtgtcttgcacccacatgcagGCCTTTGAAGCAGCATGGGCTGCAGCGTGCAAGCAGGGAGCATCTACAGTTGTCGTACCATCAGAACTTGAGTTTCTTGTTGGGCCAATCTCATTCTCTG
















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|211526105|gb|FL006816.1|FL006816
EST:     ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAG                         GCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCAT
genomic: ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCAT
EST: gi|211526110|gb|FL006821.1|FL006821
EST:     ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAG                         GCTTTTCAAGGAGCGTGGGCTGCTGGCTGC
genomic: ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGC
EST: gi|71448858|gb|DR829908.1|DR829908
EST:     ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAG                         GCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTT
genomic: ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTT
EST: gi|71772111|gb|DR970048.1|DR970048
EST:     ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAG                         GCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTT
genomic: ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTT
EST: gi|91872778|gb|EB402735.1|EB402735
EST:     ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAG                         GCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTT
genomic: ATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTT
EST: gi|211526113|gb|FL006824.1|FL006824
EST:     TGTGGGTGATTTTGGAGCCAAGGGTGANCG-ANNTACAGACGATACTAAG                         GCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCCAGGGG-CATCTACACT
genomic: TGTGGTTGATTTTGGAGCCAAGGGTGA-CGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCC-AGGGGGCATCTACACT

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 43

GTCACAGCCGCCACCACCAGCAACCTCCTCGCAGCATGGTGCAGTATTCAATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 14

GTCACAGCCGCCACCACCAGCAACCTCCTCGCAGCATGGTGCAGTATTCAATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 2

GTCACAGCCGCCACCACCAGCAACCTCCTCGCAGCATGGTGCAGTATTCAATGTGGTTGATTTTGGAGCCAAGGGTGACGGAGTTACAGACGATACTAAGgtccgatagc ... ttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtttctttcagaaatctagagccaataattgtacgtccattttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG
                                       tccatttt  CT-rich tract
                           aataattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggatacacaaacacaaatgcataatcttttccatagctcttgcaagatgtttctttcagaaatctagagccaataattgtacgtccattttgcatacagGCTTTTCAAGGAGCGTGGGCTGCTGCCTGCACCCAGGGGGCATCTACACTTCTCGTACCACCAGAACTAGAGTTCCTTGTTGGGCCAATCTCGTTCTCTG

- gatacac
- - - - -aaacaca
- - - - - - - - -atgcata
- - - - - - - - - - - - - - - - - - - tcttgca