Sequence
atgc intronic sequence ATGC exonic sequence...ctttaagtacttctatttcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 5
ctttaagtacttctatttcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaa--------cagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
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-----attac--ccataaaatcaactcatgtaattgttaatt-attatacatgaaattgtaagtctttcaatcatgagacttttctcaccaattacatttatttgcagAGGAGGCCGGGGTGGTGGGTATAAAGAACTTGATGAAGAAGAACTAGAGGAAGTTAAAAGGCGCCGCAAAGAGGCTGAAGAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 5
ctttaagtacttctatttcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtatta-ataatattttt------ttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
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--tcatgtaattattatacataaa--atggcaagtgacatct-atataactttta--tatagaattattatcatgtaacttttctcaccaattacatctctttgcagAGGTGGCCGGGGTGGTGGGTATAAAGAACTTGATGAAGAAGAACTAGAGGAAGTTAAAAGGCGCCGCAAAGAGGCTGAAGAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 5
------ctttaagtacttctatttcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
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tatgcccattaagtgagcaaccatgcatatgcatttaactatttctaaccaaaaaatgtttattcaaatatcaaggtttgccttgccttttttattt------tagGGGTGGCCGTGGTGGTGGGTACAAAGAGCTTGATGAAGAAGAACTAGAGGAAGTTAAAAAACGTCGGAAAGAGGCTGAGGAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC185415.3_FGT005 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------ctttaag-tacttctatt-------tcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
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gtgagtggttagttgtgaaccatgctgtgcatgttgtgtgaaacataatgtaaacaacgggcacactgggtgtttatatgatatgtccattaagtgagcaaccatgcatttaactatatgtaacaaaaggtgtttattca-aatatcaagGTTTGCATTGCCATTTTTCTTCATTT--TAGGGGTGGCCGTGGTGGTGGGTACAAAGAGCTCGATGAAGAAGAACTAGAGGAAGTTAAAAAACGCCGGAAAG-----------
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G11060.1 (Glycine max), 3'ss of exon 4
ctttaagtacttctatttcatcattcattctaatttttgttttataatatc-ttgaggt-gtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
| | || | ||||| || ||| || | ||| | | ||| | |||||| | | || | | | | || | ||||||||||||||||| ||||||||||||||||| ||||||||||| ||| |||| || || | | | || | |||| ||||||
gtgtctgttttactatt-cacaatttttttttctttaccaatgaaaatgttactgaggttactctcctaaggtttgttctttataatttc-taattaaacagAGGAGGACGAGGTGGAGGTTACAAAGAGCTTGATGAAGAGGAAATAGAAGAAACTAGACGTCGTAGAAGGGAAGCTGAA---
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 4
ctttaagtacttctatttcatcattc--attctaatttttgttttataatatctt---gaggt-gtaatgtcagtattaataatatttttttgggtt---gttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
||| ||| | |||| ||| | | || || | || | ||||| || | || | | ||| | || ||||||||||||||||| ||||||||||||||||| ||||||||||| ||| |||| || || | | | || || |||| ||||||
---------tgtctgttttactattcacatttttttcctttaccgatgaaatgctaccgaggttactctgctaaggtttgttcttactttctaatttctaattaaacagAGGAGGACGAGGTGGAGGTTACAAAGAGCTTGATGAAGAGGAAATAGAAGAAACTAGACGTCGTAGGAGGGAAGCTGAA---
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 5
----ctttaagtacttctatttcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
|| || | | | | |||| ||| |||| | | || | || |||| | || ||||||| | |||| || ||||| |||||||| |||||||| ||| | |||||| ||||| ||||||| || || |||||| |||| ||||||||||||
tttggccaaattagagttgcattaagaaacattaaggtttgagtttggaaggttgtttttatctag-accagtgcttattcatttttttt---tctctaaatagGGGAGGCCGTGGTGGTGGTTACAAGGAATTAGATGAACAAGAATTAGAGGAAACGAAGAGACGCAGGCGTGAGGCTGAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
tattaat putative branch site (score: 2)
tgtaatgtcagtatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttaagtacttctatttcatcattcattctaatttttgttttataatatcttgaggtgtaatgtcagtattaataatatttttttgggttgttaaacagAGGAGGACGTGGTGGAGGTTACAAAGAACTTGATGAAGAAGAACTAGAGGAGACCAAAAGACGCCGGCGGGAGGCTGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - -cattcat