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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaacgttccatggagctccacaagtctgtactgtaccaccatttagagttgtccatacaatcgtcttctgaacatttcgtctcttcggcacggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA

Basic information

species Zea mays
transcript GRMZM2G032628_T01
intron # 2
splice site 3'
intron type U2

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|6021362|gb|AW066290.1|AW066290
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|211168614|gb|FL101056.1|FL101056
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|31354729|gb|CD439086.1|CD439086
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|31363541|gb|CD447898.1|CD447898
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|211170285|gb|FL101059.1|FL101059
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|211170284|gb|FL101058.1|FL101058
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|211168615|gb|FL101057.1|FL101057
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
EST: gi|101397443|gb|EB820645.1|EB820645
EST:     GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAG                         GTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT
genomic: GCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCT

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: 45 (upstream exon), 47 (downstream exon)
Score: 54

GGCGGCCGCGGCCAGGAAGGCGGTCATGGTTCCTGAGGGCGAGAATGATGGCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 22

GGCGGCCGCGGCCAGGAAGGCGGTCATGGTTCCTGAGGGCGAGAATGATGGCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 13

GGCGGCCGCGGCCAGGAAGGCGGTCATGGTTCCTGAGGGCGAGAATGATGGCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

GGCGGCCGCGGCCAGGAAGGCGGTCATGGTTCCTGAGGGCGAGAATGATGGCCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGgttcgtcatc ... acggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttgtccatacaatcgtcttctgaacatttcgtctcttcggcacggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA
          atacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaacgttccatggagctccacaagtctgtactgtaccaccatttagagttgtccatacaatcgtcttctgaacatttcgtctcttcggcacggttccagGTACCAGACATTTCTGAAGAGACAACGTGCGGTGCTGGTGTGGCTGATGCTCAAGCCTTGAACAGAGTTCGAGTGGTCCCCCCACCAAGCGATGGACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - ccatgga
- - - - - - - -gctccac
- - - - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - - - taccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - catacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttctg