Sequence
atgc intronic sequence ATGC exonic sequence...caacagccaaacatatccctaatatttattggctatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: 13113.m00212 (Oryza sativa), 3'ss of exon 1
caacagccaaacatatccctaatatttattggctatacttttgt--tgatgaat-tattattttgatgttgtaacttagttg--attttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
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----ggtcggagatgtaaatcattttcattatctaagctctctccatcatgcatgcatggccatggaggtg-acgggggttgccatttgttgcgtgtgtgtgcagAGAGGTGCAGGATCGGGTCGGCGCCGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACCGCAAGTACCCGACGGGGTCGAGGACGAACCGCGCCACGAC
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G099144_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------caacagccaaacatatccctaat--atttattggctatacttttgttgatgaattattattttg-atgttgtaacttagttgat------------tttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
||| || || | | | || ||| || ||| | || || | | | | | ||| | | || ||| | || ||||||||| || |||| ||||| | || || || |||||||||||||||||||||||||| | ||||| || || ||||| ||||| || | ||||| |
gtatagtgcttgggcatgttacgttcatggcttcatccttcatgcatggcgattcagttacatgcacgcagcttgttgtttagttgtttgtcttagcttgttcctgtggcttcctgcacagcacggtaatactcattacatcatgctcatccacttgcatcgatcggtgcagAGAGGTGCCGGATCGGGTCGGCGCCGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACCGCAAGTACCCGACGGGGTCCAGGACGAACCGCGCCACCAC
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G435824_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------caacagccaaacatatccctaatatttattggctatactt------ttgttgatgaattattattttgatgttgtaacttagttg-attttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
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gtatatatattatatacttggcaaataaaaaccagttcatgcccccatgcatgcatgcatgtccatggcgatcaatcaatcagttactacatgcaggcgcagccatgccggctgcagcttcttcttgttgagtcgttcgtcgctcatccacgtgaatccatcgttgcattgcatgcatcggatatatatgcagAGACGTGCCGGATCGGGTCGGCGCCGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACCGCAAGTACCCGACGGGGTCGAGGACGAACCGCGCCACGAC
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 1
-----caacagccaaacatatccctaatatttattggc-tatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
| | ||| | | | | || ||| |||||||| | | | |||| ||| |||| | | | ||| ||||| | || | |||| |||||||| ||||| || || |||||||| |||||||| |||||||| ||||||||||| ||||| || ||||| ||||||||||||||||| || ||
attttacatattgaaataaaacgttttcatcaatttttacatactttttattttca-ctatt--tttagtgttttctcat-gttaatttttt-catg-acaaacagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCCACAGGTTCAAGGACTAATAGAGCAACGAA
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G36820.1 (Glycine max), 3'ss of exon 1
caacagccaaacatatccctaatattt---at-tggctatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
| | || |||| | ||| |||| || | | || | ||| || || | | |||||| || | | | ||| | ||| | | | |||| |||||||| ||||| || || |||||||| |||||||| |||||||| ||||||||||| ||||| || ||||| ||||||||||||||||| || ||
-gagaaaacaatatattcttaaaattttacatattgttacatattt-ttcatttttcactatttttattgtttgcttatgttaaattttt-cgtg-acaaacagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCTACAGGTTCAAGGACTAATAGAGCAACGAA
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G33280.1 (Arabidopsis thaliana), 3'ss of exon 1
caacagccaaacatatccctaatatttattggctatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
| ||| ||||| ||| | | | | | | | | |||| ||| | || || ||||| | | | | | || ||| ||||| | || || || || ||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||||||||| || | || || |
--gtacgttcttttattaataatacatatacgatccaatcctctagttatatta-------gatactatacaaaagc--attttttttttgtttttgtagATAGATGCAAAATAGGATCAACGCCACAAAATGAGTGGTATTTCTTCAGCCACAAGGATAGGAAATATCCGACAGGGTCAAGGACAAACCGTGCAACCCA
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
caacagccaaacatatccctaatatttat-tggctatacttttgttgatgaattattattttg--atgttgtaacttagttgat-tttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
| | | |||| || ||| ||| | | |||| | | | | ||| || | || | ||| || || | | | | ||| | | | ||||||||| | ||| || || ||||||||||| || ||||||||||||||||||||||| ||||| ||||| || ||||||||||| || | || || |
---tatatatatatatatata-tatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatctttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------caacagccaaacatatccctaatatttattggctata---cttttgtt----gatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCA-CACCAC--------AAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA-
| | || | | | |||| | ||| ||||||| ||| | ||| ||||| || | ||||||| |||| ||| | ||| ||||| ||| | |||||| | | ||| ||||||||||||||||||||||||| ||| ||||| ||| | | ||| |||||||
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgatgatattcaatttttgtggcgatgt---caggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------------------caacagcca--aacatatccctaatatttattggctatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCA---CACCA------CAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
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gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagc-atgttctcctcatctattgatagcatgaaatggtccagcagta-ttgacaaaaacttgt-tgcaccgat-cagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
attattattttgatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacagccaaacatatccctaatatttattggctatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
- - - ccaaaca
- - - - - - - -tccctaa
- - - - - - - - - - - - - - -tggctat