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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattagggaggcctcttgacaacttatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

Basic information

species Zea mays
transcript GRMZM2G086489_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 12
tgttggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattaggga--ggcctcttgacaacttatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG
|||  ||   | |  ||  | | |   |     |  ||    ||||  ||  |  |   |  ||| |   | |    | |  |||||     |||||| |  |||||||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||||||||||
tgtctgataatgtattttttgtggtcattttg-aggatatgacttgctgttctatttgttctcttgctgcaagatctgactccttgaa----tatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG
















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|13316176|gb|BG410623.1|BG410623
EST:     CTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         CAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: CTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|40334433|gb|CK368503.1|CK368503
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         --G-ATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|32929744|gb|CF034556.1|CF034556
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         --G-ATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|32929783|gb|CF034595.1|CF034595
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         --G-ATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|32929509|gb|CF034321.1|CF034321
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         --G-ATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|32832265|gb|CD971943.1|CD971943
EST:     ATCATCTCC-AA                         -A-GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: ATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|67033233|gb|CO461982.1|CO461982
EST:     ATTGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCC-AA                         -A-GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|31351811|gb|CD436168.1|CD436168
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCC-AA                         -A-GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTACTTTATGGGCC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
EST: gi|32835719|gb|CD975397.1|CD975397
EST:     CACGATACTACTCAATTTCATCATCTCC-AA                         -A-GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC
genomic: CACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCC

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), 38 (downstream exon)
Score: 31

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 45

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 49

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 68

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... tatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggtggtggtatgtaccttccattagggaggcctcttgacaacttatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG
                                  tcttgac  putative branch site (score: 68)
                                         aacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattagggaggcctcttgacaacttatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- -tggactg
- - - - - - - -ttcatat
- - - - - - - - - - - - - -tgccata
- - - - - - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - -ggtggtg