Sequence
atgc intronic sequence ATGC exonic sequence...ctttatctatattatatatatatatatatattaaaaaaaatagtcttctggatcggaaaattacaactcatgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g01830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g52500.1 (Oryza sativa), 3'ss of exon 2
ctttatctatattatatatatatatatat--attaaaaaaaatagtcttctggatcggaaaattacaact-catgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
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-tttattgtgaacctgtaccttcacagctcaacaaacgcaaatcatatactgcagttgcatacctgatctgcaccacttatatta-caatttgaatta-gcagATCATTGGCGATGATAGTGTTTGCTACTATCACGACATGATAGTGCAAATGATCAAATGGGGATACCAAGAGGGGAAAACATTATTTGGATTTGGTTATG
upper sequence: Vv01s0011g01830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G007157_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------ctttatctatattatatatatatatatatattaaaaaaaatagtcttctggatcgga-aaattacaactcatgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
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gtgaggtgggcgcgtccgtagatggcagaaccgtgcaccgttggtgttgtggacgcctacactatcctcttaagagtagtagagatttgattatgactttgatccaagccccctatgaagtgcacgaactgcatgatcttatga-tttgctctgtcttggttttgtagATCATTGGCGATGACACTGTGTACTACTATCATGACATGATAGTGGAAATGATTAAATGGGGATATCAAGAAGGAAAAACTCTCTTTGGATTTGGTTATG
upper sequence: Vv01s0011g01830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G007157_T02 (Zea mays), 3'ss of exon 1
ctttatctatattatatatatatatatatattaaaaaaaatagtcttctggatcgga-aaattacaactcatgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
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tcttaagagtagtagagatttgattatgactttgatccaagccccctatgaagtgcacgaactgcatgatcttatga-tttgctctgtcttggttttgtagATCATTGGCGATGACACTGTGTACTACTATCATGACATGATAGTGGAAATGATTAAATGGGGATATCAAGAAGGAAAAACTCTCTTTGGATTTGGTTATG
upper sequence: Vv01s0011g01830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G02570.1 (Glycine max), 3'ss of exon 2
ctttatctatattatatatatatatatatattaaaaaaaatagtcttctggatcggaaaatta--caactcatg-atgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
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-------------------gtatgcttgttttaaagtttgttgaagtgcaatgcagatatccaagcaagttattcatgaatcctatataattcttttgaacagATGTTGGGAAGTGATTCTGTGTATTATTTCCATGACATGATCGTTGAAATGCGTAAGTGGGGGTTTGAAGAGGGAAAGACGCTTTTTGGTTTTGGATATG
upper sequence: Vv01s0011g01830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G34730.1 (Glycine max), 3'ss of exon 2
ctttatctatattatatatatatatatatattaaaaaaaatagtct----tctggatcggaaaatta--caactcatg-atgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
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-------------------gtatgcttgttttaaactgagttgcttgaattgcaatgcaaatagccaagcaatttattcatgaatcctgtataattcttttgagcagATGTTTGGAAGTGATTCTGTGTATTATTTCCATGACATGATCGTTGAAATGCGTAAGTGGGGGTTTGAAGAGGGAAAGACGCTTTTTGGTTTTGGATATG
upper sequence: Vv01s0011g01830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G19860.1 (Arabidopsis thaliana), 3'ss of exon 2
-ctttatctatattatatatatatatatatattaaaaaaaatagtcttctggatcggaaaattacaactcatgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
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gtatggtttaatttctagctgttttgttttttgagctatggatgtatttgttctcaaagctttctcttttctcattgggatctttgaactctat-atgtagATTGTTGGCCGTGAGTCTGTGTACTATTTCCATGAGATGATTGTTGAGATGATCGGATGGGGATTTGAAGAAGGGAAAACCCTTTTTGGTTTTGGTTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctggatcggaaaattacaactcatgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
ttttaac putative branch site (score: 2)
ccatttctttc CT-rich tract
atgatgaattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttatctatattatatatatatatatatattaaaaaaaatagtcttctggatcggaaaattacaactcatgatgaattttaaccatttctttcgtgcagATTATTGGGCGTGATTGTGTTTATTATTTCCATGACATGATAGTTGAAATGATGAAATGGGGTTTTCAAGAGGGAAAAACACTATTTGGTTTTGGTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatttc