Sequence
atgc intronic sequence ATGC exonic sequencegtgttcatttttctatttaagtacatgtataatataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g33950.1 (Oryza sativa), 3'ss of exon 4
--------------gtgttcatttttctatttaagta--catgtataat-ataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
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gtatgggtaaaccccccccctctctctcattttaacagtcatttcttttcgttagttttgctacaggtttatatatggtttccaacaaaaacagGTTCGGAAACGGCGCATATATGACATAACAAATGTACTGGAAGGAACAGGTTTGATAGAAAAGAAGCTTAAGAACAGAATCCGTTGGAG
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
----gtgttcatttttctatttaagtacatgtataatataaattacatgctattttaatttaaggtcttt---tatacaaa--------cagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
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gttaatatttccttctgtttttttct-catatcctgtttgc-taacacgcctttattttgtcaagcttatatgtatgtaaaatgttttgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 6
-----------------------------gtgttcatttttctatttaagtacatgtataatataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
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gatgatattgatgttgactagaggttggtgctttccttttggtaccttgatccagtcatggtttcttttgttaaacatatgcatatatagctttttt------cagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 6
-----------------------gtgttcatttttctatttaagtacatgtataatataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
||| | || ||| |||| || | | | | | || | | || | | ||||| ||||| ||||| ||||||||||| || |||||||| ||||| || || || || ||||||||||| ||||||| ||||| |||||
cagatgatattgatgttgactagaggttggtgctttccttttggtacttgatccagtcatggtttcttttgttaaacatatgcgtatatagctttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G052515_T01 (Zea mays), 3'ss of exon 4
------gtgttcatttttctatttaagtacatgtataatataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
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gttggtgctttccttttggtaccttgatccaatcatggtttcttttgttaaacatatgcatttataacttttttt-----cagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAAAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G35850.1 (Glycine max), 3'ss of exon 4
gtgttcatttttctatttaagtacat---gtataatataaattacatg----------ctatttta-----atttaaggtcttttatacaa-acagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
|| | | ||| | || || || | || ||| | | || ||||| || |||||| | ||| | | |||| || |||||| |||||||||||||||| |||||| ||||||| |||||||||||||||||||||||||||||||| || | |||||
--gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
gtgttcatttttctatttaagtacatg-----tataatataaattacatg--------ctatttta-----atttaaggtcttttatacaa-acagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA-----------
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--gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
--------gtgttcatttttctatttaagt--------acatgtataatataaattac------atgctattttaatttaaggtcttttatacaa-acagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
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gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgtataatataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
ttttaat putative branch site (score: 3)
tcttttat putative PPT
tataatataaattaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttcatttttctatttaagtacatgtataatataaattacatgctattttaatttaaggtcttttatacaaacagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA