Sequence
atgc intronic sequence ATGC exonic sequence...acttgtaggatgcaacctgtcctgctacttattccagtgctattcctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------acttgtaggatgca---acctgtcctgctacttattccagt--gctattcctgcttttgcattattcttgaacttacccatatatacatggtatgttatctat--agGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
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gtactgtttcctatgcagttcaaaacttatgaacgtagcatcaatagacattaaaaaagtcagatatttaggacgaatatgtcagtattcactcttactgaattaagttgatcctgataatccatttttcatcttctgaaatggagtaattttgtcttgtatttgtgcagGTTGCCAAGGAGAGTGCAGATGTCATAGTACTTGACGATAATTTCACAACTATAATAAATGTTGCAAGATGGGGTCGTGCAGTTTATATTAACATCCAAA
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G31770.1 (Glycine max), 3'ss of exon 2
acttgtaggatgcaacctgtcctgctacttattccagtgctattcctgcttttgcattattcttgaacttacccatatatacatggt-----atgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
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-----tacgtggcggtttctttttcctctttttatattaatgactctttgctaccattcatatctagtagcattttttgtgcttgataattaataccatttacagGTTGCCAAAGAAAATGCCGATGTCATTATAATGGATGATAACTTCACGACTATTGTCAATGTTGTCAAATGGGGACGTGCAGTATACATAAACATTCAAA
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G29010.1 (Glycine max), 3'ss of exon 5
acttgtagg-atgcaacctgtcctgctacttattc-cagtgctattcctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
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--tagtagttacatcatttatttaccgactctttaatttttcctttgctgccattgatacctattaacattttttgtccttcataattaatttcatttacagGTCGCTAAAGAAAATGCTGATGTCATTATAATGGATGATAACTTCACGACTATTGTCAATGTTGTCAAATGGGGACGTGCAGTATATATAAACATTCAAA
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G15800.1 (Glycine max), 3'ss of exon 4
-acttgtaggatgcaacctgtcctgctacttattccagtgctattcctgcttttgcattattcttga----acttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
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aattcttgtcat---atttgtttcgatgtctatttta-tattattgtctggttgacgttatcaccaatactatttttccttttttaaa-attataccttttacagGTTGCCAAAGAAAATGCTGATGTCATTATAATGGATGATAACTTCACTACTATTGTCAATGTGGCCAGATGGGGACGGGCCATATACATAAACATTCAAA
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 4
acttgtaggatgcaacctgtcctgctacttattccagtgctattcctgcttttgcattattcttgaacttacccatatatacatgg---tatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
| | | | | | | ||| | | |||| | | |||| | || |||| | | ||| | | || ||| | || |||||||||||||||||||||||||||| |||||||| ||||| || | ||||| || ||||| |||| ||||| || || |||| |||||||||||||
aatccttg--tcctatttgtttcgatgtctatttta-tattattacctggttgatgttatcactaatattatttttccttttttgaaattataccttttacagGTTGCCAAAGAAAATGCTGATGTCATTATAATGGATGATAACTTCACTACTATTGTCAATGTGGCCAGGTGGGGACGGGCCATATACATAAACATTCAAA
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
acttgtaggatgcaacctgtc-ctgctacttattccagtgctattcctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
||| | | | || ||| || | || | || | |||| || | | | | | | || | ||||||| ||||| ||||||||||| ||||||||||||||||| || || ||||||||||| || | |||||| ||||| ||||||||||||||||| |
----gtaagctatagttattctctgttattggtttggttaataaaaaaatctcgagatta-------acattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 3'ss of exon 4
acttgtaggatgcaacctgtcctgctact-tattccagtgctatt--cctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
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-----------gtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactcccgcgtatacaacacacagGTTGCGAAAGAGAATGCTGATGTTATCATAATGGACGACAACTTTGCAACAATAGTGAATGTGGCAAAATGGGGACGTGCTGTGTATATCAACATCCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
aacttac putative branch site (score: 2)
atatatacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttgtaggatgcaacctgtcctgctacttattccagtgctattcctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA
- - - -ggatgca
- - - - - - - -cctgtcc
- - - - - - - - - - - tgctact
- - - - - - - - - - - - - - - - -ccagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgg