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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgatattttcactttattcttcttacctgatcttgttttagtgtatgtcatttcaaactttctgtttgttaaaatttttatgagtcatttgtaaatttccacatgttatctttggtcttagtgtgcattcttcaattatgctaattaatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG

Basic information

species Zea mays
transcript GRMZM2G095239_T01
intron # 3
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|89761715|gb|DY689620.1|DY689620
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
EST: gi|211130407|gb|FL313028.1|FL313028
EST:     GCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: GCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
EST: gi|76287133|gb|DV026701.1|DV026701
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
EST: gi|78105940|gb|DV524358.1|DV524358
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATG
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATG
EST: gi|50329506|gb|CO524632.1|CO524632
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
EST: gi|74244193|gb|DT652107.1|DT652107
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
EST: gi|60359172|gb|DN226145.1|DN226145
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
EST: gi|76280710|gb|DV020278.1|DV020278
EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATC

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: 94

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 69

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 119

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgttatctttggtcttagtgtgcattcttcaattatgctaattaatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG
                                 aattatgctaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgatattttcactttattcttcttacctgatcttgttttagtgtatgtcatttcaaactttctgtttgttaaaatttttatgagtcatttgtaaatttccacatgttatctttggtcttagtgtgcattcttcaattatgctaattaatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA