Sequence
atgc intronic sequence ATGC exonic sequence...ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaaaacgcactatattttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 27
ttattccttgcaagttaccatcgac-tatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaaaacgcactatattttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
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gtgaccaggataaacataaataaacgtgaatttttcaa--tgaccttttcttctg-acatctgaatctgatgaatttcttg---catattaa----tacagTTGGCACTTAAAGCTAGTGAACTTCTTGAACAAACAAAACTTAGTGAGCTCCGTGCAAGAATAGCAAGGAGCCTTTCAGAGCTGGAGATGTTTACTGAGG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 25
ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaaaacgcactatattttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
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-----------gtgcggtgattagaaataacctagatattccccttataaattattttgatattttacctaatgaattccatgcatcttaataaacacagTTGGCCCTTAAAGCAAGTGAACTTCTTGAACAAACCAAACTAAGTGAACTCTGTTCCAGCATTGCAAGAAGCCTTTCAGATCTGGGGATGCATAAGGGAG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 25
ttattccttgcaagttaccatcgactatccttttcaa-gttgatgtcatgatttatatatatatatttttaaatgttctcaaaacgcactatattttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
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-------gtgca-gtggttagaaataacttagatagatattcccattataatttattttgatatttttcctaatgaattccatgcatcttaataaacacagTTGGCCCTTAAAGCAAGTGAACTTCTTGAACAAACCAAACTAAGTGAACTCCGTGCAAGCGTTGCAAGAAGCCTTTCGGATCTGGGGATGCATAAGGGAG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G377341_T01 (Zea mays), 3'ss of exon 22
ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatat-atatttttaaatgttctcaaaacgcactatattt--tgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
|| ||| | || | || || || | | || | | | || || || | ||| | || | | | | || ||||| ||||||| || ||||| ||||| || || || || ||| ||||||||||||| ||||||| |||||||||||||| || | |||||||||||||| |
gtaaag-ttgaagattttgaaagattaaagtt--cgatttattttgctcatgtagtcatgtgatagctgataaaaaatgtgtgatatattgttattgatgcagCTGGCACTTAAAGCAAGCCAACTTCTTGAGCACACTAAATTGAGTGAACTTCGCACCAGCATAGCAAGAAGCCTTTCAGAGCTGGAGATGTTTACTGAGG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 24
ttattccttg-caagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaa-atgttctcaaaacgcactatattt--tgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
||| | | | | ||| | | | || | || | |||| | | | | | | | ||||| | || | | | | || |||||||||| ||||||||||||||||| ||||||||||| ||| | ||||||||||| |||| |||||| ||||| |||||||| |||||||||||||| || |
-tatccttcgattatctacttttg--tttcatcttgtggatgatacttttacatctttgga-acattttgagtgaaatcctggtttgtaattttgttgatgcagTTGGCTCTAAAGGCAAGTCAACTGCTGGAACAAACTAAATTAAGTGAACTTCGATCCAACATTGCTAGAAGTCTTTCTGAGTTAGAGATGTTTACAGAGG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 24
-----------------------------------------------------------------------ttattccttgcaagttaccatcgactatcc-ttttcaagttgatgtcatgatttatatatatatattttta-aatgttct---caaaacgc--act--atatttt------gcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
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gttggacattaccctgagaaattgagttccaagttatattttttggacataccatttcttctactgggagagcattgtgaatatatatccttcaattatctacttttggtttcatcttgtggatgatacttttacatctttggaacattttgagtgaaatcctgatttaaaattttcttgatgcagTTGGCTCTAAAGGCAAGTCAACTGCTGGAACAAACTAAATTAAGTGAACTTCGATCCAACATTGCTAGAAGTCTTTCCGAATTAGAGATGTTCACAGAGG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 24
ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaa--aacg--cactatat-tttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
| | ||| |||| | | ||| |||||| |||| ||| | | |||||| || | || | | | | || ||||||| || ||||| |||||| |||| ||||| |||||||| ||||| |||||||| | |||||| ||||||||||| || ||||| |||||||| || |
--------------------------gtgcgttt--ggttgct-ttatgttttata---atatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 24
ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaaaacgcactatattt-tgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
|| | || | ||| | ||||| | | | | ||| | | || | | | ||| || || ||||||| || ||||| |||||| | || ||||| ||||||| || ||||||||||| | ||||| ||||||||||| |||||||| |||||||| || |
------------------gtgcgtttggttcctttatgtt----ttatgatacttttgttgacattcgtcag----ctgatgattga-tatgttcgtgtagTTGGCGCTCAAGGCGAGTCAATTGCTCGAACAGACCAAACGAAGCGAACTTCGTTCAAATATTGCTAGAAGCCTTTCAGAATTAGAAATGTTTACAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgatttatatatatatatttttaaatgttctcaaaacgcactatattttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
tttatatatatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaaaacgcactatattttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - -ccttgca
- - - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacgc