Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttatccaaaaagtgttccgtaatgttctctaatgttcttgtagatgtctccgataacgtggattttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G451366_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 5
gtatgtttatccaaaaagtgttccgtaatg--ttctctaatgttcttgtagatgtctccgataa-cgtggattttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
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gtacgtcttcgtgaaaaatgtttc-tagtgccttctttaatattcttctagatattttgcataaatgcatattttctcagGCACTTTCTGTGGGAAGCGACAGCAACGGGAGTGGAGCTGTGGCTCTTCTAGAGATTGCAAGACTGTTTTCACGCCTCTATTCAAATCCTAAGACCAGAG
upper sequence: GRMZM2G451366_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G44330.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtttatccaaaaagtgttccgtaatgttctctaatgttcttgtagatgtctccgataacgtggattttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
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------gtatgtaatatgagtagtggatcttcttaccgtaatatcaagtacatacctgacaaacttg-tatatgtagGCATTATCAGTTGGAAGTGACAGCAATGGAAGTGGGGTTGTGGCGCTTCTTGAAGTGGCTAGATTATTTTCCGTTCTGTACTCAAATCCCAAGACGAGAG
upper sequence: GRMZM2G451366_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0080g00880.t01 (Vitis vinifera), 3'ss of exon 5
----gtatgtttatccaaaaagtgttccgtaatgttctctaatgttcttg---tagatgtctccgataacgtggattttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
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gtatgtattttcctttttaacattcctatctaaataaataaactttttagccatataaatgtctgagaaaatatatttttt-agGCATTGTCAGTGGGAAGTGATAGCAATGGAAGTGGAGTTGTGGCACTTCTTGAGATAGCTAGGTTATTCTCTCTACTTTATTCAAATCCTAAGACAAGAGMapped 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|148957547|gb|EC903641.2|EC903641EST: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCT GCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
genomic: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
EST:
gi|211532947|gb|FL381078.1|FL381078EST: CTATGACACCTTCGGTGCTGCACCT GCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
genomic: CTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
EST:
gi|60339357|gb|DN206330.1|DN206330EST: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCT GCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
genomic: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
EST:
gi|32921841|gb|CF026653.1|CF026653EST: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTTGGTGCTGCACCT GCACTTTCTGTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
genomic: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
EST:
gi|71440389|gb|DR821439.1|DR821439EST: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCCGTGCTGCACCT GCACTTTCTCTGG
genomic: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGG
EST:
gi|61119699|gb|DN560660.1|DN560660EST: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCT GCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
genomic: TTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTA
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:
95GGATGGTTACCTGGATTGAAAGGAGAGGGTGATAGTGAACAGCTTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
66GGATGGTTACCTGGATTGAAAGGAGAGGGTGATAGTGAACAGCTTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
106GGATGGTTACCTGGATTGAAAGGAGAGGGTGATAGTGAACAGCTTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
96GGATGGTTACCTGGATTGAAAGGAGAGGGTGATAGTGAACAGCTTCCGACTATTGCCATAGTTGCAAACTATGACACCTTCGGTGCTGCACCTgtatgtttat ... attttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgtaatgttctctaatgttcttgtagatgtctccgataacgtggattttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
cgataac putative branch site (score: 96)
ttttctc putative PPT
taatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttatccaaaaagtgttccgtaatgttctctaatgttcttgtagatgtctccgataacgtggattttctcagGCACTTTCTCTGGGAAGCGACAGCAATGGAAGTGGAGTTGTGGCTCTTCTAGAGATTGCAAGACTATTTTCACGTTTGTATTCAAATCCTAAGACAAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA