Sequence
atgc intronic sequence ATGC exonic sequence...gagaaaggcagtctatgcaatcttcaaatacattaaatgtgagcctatcagcagccaatttcgctaggatgaaacactgaagttatttaattgattgcagCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0014g01460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g48280.1 (Oryza sativa), 3'ss of exon 6
gagaaaggcagtctatgcaa--tcttcaaatacattaaatgtgagcctatcagcagccaatttcgctaggatgaaacactgaagttatttaattgattgcagCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT----------
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-atgtgtttttccaacaaaaactcttgagcattgtcaactattggaagttaggggtatcactttgctatacttaccttgtgacaacactctttttttt-cagTATCCAGGCACTCCTAAGTGCACCAAACCCTGATGATCCTCTCTCTGATAACATTGCAAAGCACTGGAAAGCCAATGAAGCAGAAGCTGTTGAAACAG
upper sequence: Vv19s0014g01460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G35790.5 (Glycine max), 3'ss of exon 6
----gagaaaggcagtctatgcaatcttcaaatacattaaatgtgagcctatcagcagccaatttcgctaggatgaaacactgaagttatttaattgattgcagCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT------------
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tggccacaacgctgtattgtaaatcagtgaaaaatattaacc-tgctcttgactgtgaagattattgttataatgggattttt---ttgtggatccttttccagTATTCAAGCTCTTCTAAGTGCACCTAACCCAGATGATCCACTTTCTGAGAACATTGCCAAGCATTGGAAATCTAATGAGGCCGAGGCTGTTGAAACAGGT
upper sequence: Vv19s0014g01460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G35790.4 (Glycine max), 3'ss of exon 6
----gagaaaggcagtctatgcaatcttcaaatacattaaatgtgagcctatcagcagccaatttcgctaggatgaaacactgaagttatttaattgattgcagCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT----------
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tggccacaacgctgtattgtaaatcagtgaaaaatattaacc-tgctcttgactgtgaagattattgttataatgggattttt---ttgtggatccttttccagTATTCAAGCTCTTCTAAGTGCACCTAACCCAGATGATCCACTTTCTGAGAACATTGCCAAGCATTGGAAATCTAATGAGGCCGAGGCTGTTGAAACAG
upper sequence: Vv19s0014g01460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S238_21V6.1 (Physcomitrella patens), 3'ss of exon 6
gagaaaggcagtctatgcaatcttcaaatacattaaatgtgagcctatcagcagccaatttcgctaggatgaaacactgaagttatttaattga--ttgc-agCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT----------
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gacgaacacgggttaatagaactgtagataggttcga-gttcattttttacctgtatacagcactgtaatg--acattgtattcttctggtgggggttgccagCATTCAGGCTTTGCTAAGTGCACCTAACCCAGATGATCCTCTGGCTGAAAATATCGCTAAACACTGGAAGACAAACGAACAGGAGGCTGTGGAGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcagcagccaatttcgctaggatgaaacactgaagttatttaattgattgcagCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT
aattgat putative branch site (score: 4)
aagttatttaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaaaggcagtctatgcaatcttcaaatacattaaatgtgagcctatcagcagccaatttcgctaggatgaaacactgaagttatttaattgattgcagCATTCAAGCACTACTAAGTGCTCCAAACCCGGATGATCCTCTTTCTGAGAACATTGCTAAGCATTGGAAGACAAACGAAGCTGAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
gagaaag
- - - - - - ctatgca
- - - - - - - - - - - - caaatac
- - - - - - - - - - - - - - - - - - - - - -cctatca
- - - - - - - - - - - - - - - - - - - - - - - - - gcagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacac