Sequence
atgc intronic sequence ATGC exonic sequence...tggcactgtttattgcaattttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 1
--tggcactgtttattgcaattttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
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ggcgattgaatttgccaaaattttga-cgagaagctactgtcact-attgtctacttccttaaatactatgttgctgatgttgagggtatgttcgatgtcagGTGATGCCCTATATAGTCTGCGCCAAAGTCTGAAAGATGCTAACAATGTGCTGCAGAGTTGGGATCCCACTCTGGTCAATCCATGCACATGGTTCCATGT
upper sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g07760.1 (Oryza sativa), 3'ss of exon 1
-----tggca-ctgtttattgcaattttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
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ctacacaacaattattagctactattt-atgcacaatcctcattgattgtttggttaaattttattcacctgttgttgatacatgatt-----ctattattggcagGTGATGCATTGCATAGCTTGAGGACTAATTTAGTTGATCCTAATAATGTTCTACAAAGTTGGGACCCAACTCTGGTCAATCCGTGCACTTGGTTTCATGT
upper sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 1
tggcactgtttattgcaattttaaatgggatgccggtgaaattcactatc-gctgttgatgtttctaa-tgatgacg---atctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
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---tatctagggatacagttttttttttgat--tgacgcactcctttgtttgcgagtgacatttctgactaaagaagtatgtattttccattctgctattgacagGTGATGCCTTGCATAGCTTGAGGACTAACTTAAATGATCCTAATAATGTTCTACAAAGTTGGGATCCCACTCTGGTCAACCCCTGCACTTGGTTTCATGT
upper sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G870959_T01 (Zea mays), 3'ss of exon 1
tggcactgtttattgca-att--ttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
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-atcgttactaacggcatattaatgaaggggaaagcttatgcatcctattaaatgtcttg-tgtgtagattattgcttattgtgatgatacctcaatg-gcagGTGATGCTCTATACAGCCTACGACAAAGCCTGAAAGATAACAACAACGTGCTGCAGAGTTGGGATCCAACTCTGGTTAATCCATGTACATGGTTCCATGT
upper sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G115420_T01 (Zea mays), 3'ss of exon 1
tggcactgtttattgcaattttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttg----------cttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
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----------tattttgcatacaagctcatcaccgataaaagttcttatctgtttgttcatcttaactgggaatatacttgctgctgataatgttaccttttgtccacagGTGATGCCCTGTACAGCCTGCGTCAGAGCTTGAAAGATGCTAACAATGTCTTGCAGAGTTGGGATCCCACTCTTGTTAATCCATGTACATGGTTCCATGT
upper sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 1
tggcactgtttattgcaat-----tttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
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agcctctaatctcagagaggcctgtttgaatagttctctcttgaaattagacttttcaccaattgatgctaattgtgtagat----ttgttgttcttgtta-tagGTGATGCTTTGCATACTTTGAGGGTTACTCTAGTTGATCCAAACAATGTCTTGCAGAGCTGGGATCCTACGCTAGTGAATCCTTGCACATGGTTCCATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
ttctaat putative branch site (score: 2)
tctttttcttgctttt putative PPT
tttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggcactgtttattgcaattttaaatgggatgccggtgaaattcactatcgctgttgatgtttctaatgatgacgatctttttcttgcttttgtaagcagGTGATGCTTTGCATAGCCTAAGAACCAATTTAGAAGATCCTAACAATGTGCTGCAGAGTTGGGATCCTACGCTAGTGAACCCATGCACATGGTTTCATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - -ggatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgac