Sequence
atgc intronic sequence ATGC exonic sequence...atatgttgatgacttgtgcctgccagtcatttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtttctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 4
--atatgttgatgacttgtgcctgccagtcat-ttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtttctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
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tgattttgtggttgcatatttattctttttaaatctatggtgaacaattattct--cgatcttaaatggaatctcaagatattttgcttcaaattt-ctgcagATAAGCTTCCAGGAATTCAAGAATAAGCTACTAGAACCTGGTTTAGTTGACCGCATTGTTGTTTCAAATAAATCAGTGGCAAAGGTCTATGTCAGGAGTT
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 4
--atatgttgatgacttgtgcctgccagtcatttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtt-tctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
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gcaaagaaggactgcttgca--tagcagtcgttgccccttcta-agtgtgcgtactatagtataatggttcgttataatgtcttttgtatcaaacatctgcagATAAGCTTCCAAGAGTTCAAGAACAAGTTACTAGAACCTGGTTTAGTTGATCGCATTGTTGTTTCAAATAAATCAGTAGCGAAGGTCTACATCAGGAGTT
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 4
atatgttgatgacttg-tgcctgc-cagtcatttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtt---tctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
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-----ttggcaacaagatacctgttcatttgtgtctggttttatggtttcttttatttcattgttatcatctttctgacatgaatcagaatttgattctttgcagATTAGCTTTCAGGAGTTTAAAAACAAGCTTTTGGAACCAGGATTAGTAGACCATATTGTTGTCTCAAATAAATCAGTTGCCAAAGTATATGTAAGGAACA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 1
atatgttgatgacttg-tgcctgc-cagtcatttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtt---tctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
||| || | | |||| | | | || |||| ||| | | ||| | | |||| | | | | | || ||||||||||| || || |||||||||||||||||| |||||||||| || || ||||| || ||||| || |||||||||||||| || || ||||||||| |
-----ttggcaacaagatacctgttcgtttgtgtctggttttatggtttcttttatttcattgttatcatctttctgacatgaatcagaatttgattctttgcagATTAGCTTTCAGGAGTTTAAAAACAAGCTTTTGGAACCAGGATTAGTAGACCATATTGTTGTCTCAAATAAATCAGTTGCCAAAGTATATGTAAGGAACA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 1
atatgttgatgacttgtgcctgccagtcatttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtt---tctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
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--accagcaaggtacctgttcgtctgt-gtctggttttatatggtttcttttatttcattgttatcatctttctgacgtggatcagaatttgattctttgcagATCAGCTTTCAGGAGTTTAAAAACAAGCTTTTGGAACCAGGATTAGTAGACCATATTGTTGTCTCAGATAAATCAGTTGCCAAAGTATATGTAAGGAACA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
----atatgttgatgacttgtgcctgcca-gtcatttcattt----tttccaatttgcctgtctacatatgatttagctttttaatgttggtttctgaatat-gttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
|| || | ||| || | | || || | | | || || | | | ||| ||| | || | | | | ||| ||| ||||| |||||||| ||||| ||||||||||| || || || ||||| || |||||||||| |||||| || |||||||| ||||| || || || ||| ||
gcaagcatattta-aactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 4
--atatgttgatgacttgtgcctgccagtcatttcattttttccaatttgcctgtctacatatgattta-gctttttaatgttggtttctgaatatgttg---cagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
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gcaagcatgtccaactatactctgtgtatcatgttatctatataactgcagacgtgtgggcctgaggaatgtcaactaattatccgtgttatatttgttggttcagATTAGTTTCCAGGAGTTCAAAAACAAGCTCCTCGAGGCTGGTTTAGTGGATCACATAGATGTTTCCAATAAAGAAGTCGCAAAAGTCTATGTGAGGAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcctgtctacatatgatttagctttttaatgttggtttctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
ttttaat putative branch site (score: 3)
atttagctttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatgttgatgacttgtgcctgccagtcatttcattttttccaatttgcctgtctacatatgatttagctttttaatgttggtttctgaatatgttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - -tgacttg
- - - - - - - - -gcctgcc
- - - - - - - - - - - - - - - - - - - - - - - tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggt