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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcaagttgaaagttcatttctagagtcctgatgtgtaccaggttccaagttcataaaagggcagcattataacttgtttattgatgcaaatgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT

Basic information

species Zea mays
transcript GRMZM5G876898_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876898_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 1
-ggcaagttgaaagttcatttctagagtcctgatgtgtaccaggttccaagttcataaaagggcagcatt--ataact-tgtttattgatgcaaatgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT
  ||   |     |||   |  ||| |  | | | |  || |   |   ||  | || ||    |   ||   | ||    ||  ||| |    |    | ||||| |||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| |
cagcctttgtggggttttatcatagtgatcagcttt-cacta---ttacagcacgtagaaatttaatttttcctgacggcattacttgtttttcacacgaacagGGACCTCTTGCTGCACCAACTCTCCAGTTGCTGACAAAAGAAGATTTAAGCAAAATGTATTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCTT

upper sequence: GRMZM5G876898_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S91_92V6.2 (Physcomitrella patens), 3'ss of exon 1
-------ggcaagttgaaagttcatttctagagtcctgatgtgtaccaggttccaagttcataaaagggcagcattataacttgtttattgatgcaaatgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT
       | | |  |  |     |||  |  || |||     |   ||||    ||||   |     ||||   | |  |   |    |   ||      |  |||||||||||| || |       ||||||    || || || || ||| | ||||| ||||| ||||||||||||||||| |||||||||||||| |  |  |
ggatttagcccatctcgagaagtatt--tgaagccctttctggcctcagg---gaagtcggtcgggtggcacattcacgatgagcgc-tccctgttggc-tttgcagGGTCCTCTGGCGGGCGAAGTTCTGCAAAAACTCACCAAGGAGGATCTCAGCAAGATGTATTTCAGTGACTTCAAGATTATTGACATCAATGGCTCCGAGT
















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|6057020|gb|AW091425.1|AW091425
EST:     GGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAG                         GGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGC
genomic: GGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAGgtcactgccc ... atgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGC
EST: gi|14883564|gb|BI273419.1|BI273419
EST:     GGGACGTCAAGCGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAG                         GGTCCTCTTGCTGCACCAACTCTGCA
genomic: GGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAGgtcactgccc ... atgtaagcagGGTCCTCTTGCTGCACCTACTCTGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 127

GGACCTCGCCCACATCGAGGCGCACATGGAGGCCTTCAACAAGAAGGGCGGGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAGgtcactgccc ... atgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GGACCTCGCCCACATCGAGGCGCACATGGAGGCCTTCAACAAGAAGGGCGGGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAGgtcactgccc ... atgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GGACCTCGCCCACATCGAGGCGCACATGGAGGCCTTCAACAAGAAGGGCGGGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAGgtcactgccc ... atgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 309

GGACCTCGCCCACATCGAGGCGCACATGGAGGCCTTCAACAAGAAGGGCGGGGACGTCAAGTGGCACATCCACGACGACCGATCGCTGCTCGCATTGCAGgtcactgccc ... atgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagttcataaaagggcagcattataacttgtttattgatgcaaatgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT
                     attataacttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcaagttgaaagttcatttctagagtcctgatgtgtaccaggttccaagttcataaaagggcagcattataacttgtttattgatgcaaatgtaagcagGGTCCTCTTGCTGCACCTACTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - -ttcattt
- - - - - - - - - - - - - -cctgatg
- - - - - - - - - - - - - - - - - tgtacca
- - - - - - - - - - - - - - - - - - - - - - - - - - cataaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca