Sequence
atgc intronic sequence ATGC exonic sequencegtttatcacaaatctttttatgtaaatttgtctctccgcattttcttgcatttgacctttgttgtgttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 3'ss of exon 14
gtttatcacaaatctttttatgtaaatttgtctc--tccgca-ttttcttgcatttgacctttgttgtgttat----tgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
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gtttat-acacatcctttcaagggaaaatagcaaaatccacagcattctagcttttgacctttgttacattgtgttttgcagTATGCAGAAGATGTTGAAAGTGGTTCTTCAGATGTTGAGACGAAGTACAAGAAAATGTATGAGGATGACATAAATCCTTTTGCTGCTTTTTCAAAGAAG
upper sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA07G09890.3 (Glycine max), 3'ss of exon 15
-----------gtttatcacaaatctttttatgtaaatttg----------tctctccgcattttcttgcatttgacctttgtt-gtg-ttat---tgcagTACGCAGAAGATATTGAAAGTGGTTCT---TCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
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gtttttaatgtgttcttaaaacatcattctatttcagtcttcaagataacctttttcccttttaccctgaactcaagatttgtttgtgattatatgtacagTATGCTGAAGATCTTGAAAGTGGTTTCGCGTCAGATGTTGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA--
upper sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 15
---gtttatcacaaatctttttatgtaaatttgt-----ctctccgcattttcttgcatttgacctttgttgtgttattgcagTACGCAGAAGATATTGAAAGTGGTTCT---TCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
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gtatcttatcgcaattctatgcttattaaattatggttgtcatttcctctttcttaaatttcatcttctttaatcatgttcagCATTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAA--
upper sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 14
lower sequence: PP1S1_786V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------gtttatcacaaatctttttatgta--aatttgtctctccgcatt---ttcttgcatt-tgacctttgttgtgttattgc-agTACGCAGAAGATATTGAAAGTGGTTCTTC---TGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
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acattgagaaatagccttttggtt-ccataactgttactaagcaccgaatggcaacagtttattaatttcttaagtcatcaactttgt-gtctgatcaccagCGCGGGGAGGATTTGGAATCAGGAATGGGGGGTGATGTAGAGAGCAGATACAAGAAGATGTATGAAGATGATATTAATCCGTTTACTGCTTTTTCAAAGA--
upper sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 14
lower sequence: EFJ26077 (Selaginella moellendorffii), 3'ss of exon 15
gtttatcacaaatctttttatgtaaatttgtctctccgcattttcttgcatttgacctttgttgtgttattgcagTACGCAGAAGATATTGAAAGTGGTTC---TTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
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--------------gttttccataa-ttttttactc----tttttttg--tctaatgtttac-acgtaatt-cagAAAATCGATGATCTGGAAGGTGGCATGGTCTCAGATATTGAATCGAAGTACAAGAAAATTTACGAAGATGACATAAACCCTTTCGCTGCGTTTTCAAGAA--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|31359186|gb|CD443543.1|CD443543EST: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAG TACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
genomic: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
EST:
gi|67019074|gb|CO447823.1|CO447823EST: ATGTCCAAGACTATANCCACGACAAGATTGTTTCCAGGGGACCAAAAAAG TACGCAAAAGA
genomic: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGA
EST:
gi|13382114|gb|BG458789.1|BG458789EST: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAG TACGCAGAAGATATTGAAAGTGGTTCTTCTGCTGTTGAAGCAAAGTACAAG
genomic: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
EST:
gi|60672578|gb|DN475280.1|DN475280EST: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAG TACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
genomic: ATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
EST:
gi|13381917|gb|BG458592.1|BG458592EST: TATAGCCGCGACAAGATTGTTTCCAGGGGACCAAAAAAG TACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
genomic: TATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
EST:
gi|6994176|gb|AW453390.1|AW453390EST: AAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAG TACGCAGAAAATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
genomic: AAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAG
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:
47 (upstream exon),
49 (downstream exon)
Score:
131ACTGGAAAAAACTAAAGCTGATAATGTGCAACTGTATGGAAAGATTCGATATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
98ACTGGAAAAAACTAAAGCTGATAATGTGCAACTGTATGGAAAGATTCGATATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
156ACTGGAAAAAACTAAAGCTGATAATGTGCAACTGTATGGAAAGATTCGATATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
Block sizes:
47 (upstream exon),
45 (downstream exon)
Score:
124ACTGGAAAAAACTAAAGCTGATAATGTGCAACTGTATGGAAAGATTCGATATGTCCAAGACTATAGCCACGACAAGATTGTTTCCAGGGGACCAAAAAAGgtttatcaca ... gttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaatttgtctctccgcattttcttgcatttgacctttgttgtgttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
atttgac putative branch site (score: 124)
attttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttatcacaaatctttttatgtaaatttgtctctccgcattttcttgcatttgacctttgttgtgttattgcagTACGCAGAAGATATTGAAAGTGGTTCTTCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG