Sequence
atgc intronic sequence ATGC exonic sequence...catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgtaatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgtaatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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--------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaa-------atctttttgacaagtgatcat-tctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttt---tttctgtaatgttc--atattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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--ttata-gtattttgggtatctatatgaatggtg---tttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactt--tatttttttctgtaatgttc--atattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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-----ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
---------------------------------------catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgt-------aatgttcatattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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gtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaatt--gtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G34920.1 (Glycine max), 3'ss of exon 5
-------------------------------------catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatg----cctggggactttatttttttctgtaatgttcatattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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gtaagttaattactattatgtagaattttatttttttgatagtgagtgtaattgtaatttttgaaatcatacttatttaatcgtccaatgattttcttgtgtgtgtatatgcttata-aatatgaatgtataaatgttgcagGCGTATTCTACGGTTGGTACACCGGATTATATTGCTCCAGAAGTTCTAATGAAAAAAGGTTATGGGATGGAATGTGATTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttt--------------tctgtaatgttcatattcgaacttgc-----agGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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gtatgtttacctcttctttttctgcgcattcttctttcctccaaactactccttgatcgtatggttaataaatggtattccagtacctg-cgcgcgagaattcacgcgcgt-acattctttttagatatatgacctgtggtttttatttttcgaccactagtcaaacatcaagtattaattccaggttttgctcatcagGCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------------------------catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggacttt------atttttttctgtaatgttcatattcgaacttg-cagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtat---acattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgtaatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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------------------------------------gtgcgtagcttgtacttccttttgtcccgatttttatcta-agtgttctt--------taacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctgg---ggactttatttttttctg--taatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
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--------------------------------------------------gtgcgtagcttgtacttccttttgtcccgatttttatctaagtttcctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcaatgcctggggactttatttttttctgtaatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
tttatttttttctgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgtaatgttcatattcgaacttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - -agaaaaa
- - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - tcctctc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcctgg