Sequence
atgc intronic sequence ATGC exonic sequence...agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
agcatctgta-catcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
| |||||| | | | | | | | | || ||| || | | | | | | || | | | | | | | | || ||||| ||||| ||||||||||||||||||||||| ||||||||||| || || |||||||||||||| || | | | ||||||||||||| |||
actttctgtagtagtgaaaagaagagagaactttcgctagatttttctcgatgtgattgctgcctggataat-attgtactgttgctttctgattttgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 3
agcatctgtacatcagcattcaatgggtattc---aatcccctttgttcacgttatcctaggatcattattatttgctca--aatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
|||| ||| | || | | ||| | | | | | | || | ||| | || ||| | | | || || |||||| || || |||||||| ||||||||||| |||||||||||||| |||||||| ||||| || || | ||| | | ||||| ||||| |||
-----ctgtgcatgtgtcttgtttagcctttcggggaatttgtgcctggaatcttttttaactttattctgatcatgtcatgacttttttttcttcatttgtcagTCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattatt--atttgctcaaatctgacagtggca------------cttct-cagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
||| || | | |||| | || | | | ||| ||||| |||||| ||| ||| ||| | | || | |||| |||||||| || || ||||||||||||||||| ||||| ||||| ||||| || ||||| || ||||| | ||| | |||||||||||||||||
--------------taaatttcatttgcttacaatacactatactggcattactttagga-cattatctggtttactctaataagcaaatgataaaagacaatctttttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaa--atctgacagtggcactt-ctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
| | | || || | || | | ||| | | | || | | | || || | | | | ||| ||| | | | |||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| ||| ||||| || |||||||||
atagtggattttacaacaatagatagatg---aattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgct-caaatctgacag---tggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
| | | ||| | | | ||| | | | | || || | || | | |||| ||| | || ||||||| | || | | || |||||||||||||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| ||| |||||| || |||||||||
---aaatagaggtcatccatgtacaagtaatgacacatcaaggtccat-taatagttgatcaattactatatcctacaaatctaatagattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcactt-ctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
|| || || || | | | | ||| | |||| || | | | | || || ||| ||| | || | |||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| ||| ||||| || |||||||||
tacaatagtggatttacaacta-tagatgatcattgtttcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 5
agcatctgtacatcagcattcaatgggtattcaatcccctttg-ttcacgttatcctaggatcattattatttgct-caaatctgacag---tggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
| | | || | || |||| || || || | | | ||| | | | || ||||| | | || | | || |||||||| ||||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| ||| |||||| || |||||||||
----tttttctttcgtcctttgtattctattttattttaaagaatttgaattgtttt-gatcaatttctgtatcctgcaaatgtaatagattttgttattggcagTCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
----------agcatctgtacatcagcattcaatgggtattcaatcccctttgttca--cgttatcctaggat-cattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
| | ||| | | | ||| ||| || | || || || || | || || ||| | | || | || |||||||| || ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| ||| | | | || ||||| |||||||||
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------------------------agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttct------cagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
|| ||| | | || | || | | | || | | | || | | ||||||| | | | || |||| |||||||| || |||||||| |||||||| ||||||||||| ||||||||||||||||| ||||| | | | | || ||||| |||||||||
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgct--ttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
----agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
| | | | | || | | || || | | ||| || | | | | | | | | | || | | | ||||||||| || |||||||| |||||||| ||||||||||| ||||||||||||||||| ||||| | | | | || ||||| |||||||||
tcttatcgttcatgc-tctttaccta-catgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtatt--aactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacgttatcctaggatcattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
atctgac putative branch site (score: 3)
cacttctc putative PPT
atcattattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
-gcatctg
- - - - - catcagc
- - - - - - - - - - caatggg
- - - - - - - - - - - - - - - - - tcccctt