Sequence
atgc intronic sequence ATGC exonic sequence...ctctccatccctctttccctctatgtttgtctctcacacatgcaagtgcatggatgtacccatgcaaatttctcctcatctaacctttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0229g00110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g41030.3 (Oryza sativa), 3'ss of exon 1
--ctctccatccctctttccctctatgtttgtctctcacacatgcaagtgcatggatgtacccatgcaaatttctcctcatctaacctttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
| | | | || ||| | | || | ||| ||| ||| || | || | | ||||| ||| | |||||||||||||||||||| ||||||||| ||||| ||| | | |||||||||||||| | ||||| || | | | | ||| || |
aaatgcttagcttggtcgaaagtctccttagtccactttaattattgatgttttcttgttgttg-gcagttttgtctctactgaattactaca-ccttgcagGCAAACACCCATGGATTATGATGATTCTGATTTTCAGAGCCAGAATTTCCAGTTAGCTGGTGAAGACAACAATAAATTCCCAGCAGGTCTGCGGCAATTT
upper sequence: Vv00s0229g00110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033478_T03 (Zea mays), 3'ss of exon 1
-----ctctccatccctctttccctctatgtttgtctctcacacatgcaagtgcatggatgtacccatgcaaatttctcctcatctaacctttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
| | || | ||| | || |||| ||| || | ||| || | | || || || | || | || | ||| | ||||||| |||||||||||||| ||||||| | ||||||||| |||||||| ||| ||||||||||||| ||| |||||| | | | ||| | |||| |
caatgattttcacacatctgcctgggtagttttg-ctcccatatatg-aattatgtt-atatataaatatggttctccgat-attttttgcttgtatt-ttgtagGCATACACCCATGGATCATGATGATACTGATTTTCAGAGCCAAAACTTTCAACTAGCTGGTGAAGGCAGTAACAAATTCTCATCAGGTTTGCGACCATTT
upper sequence: Vv00s0229g00110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G03650.1 (Glycine max), 3'ss of exon 1
ctctccatccctctttccctctatgtttgtctctcacacatg-caagtgcatggatgtacccatgcaaatttctcctcatctaacct-ttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
||| || ||| | |||||||| | || || || || | | || |||||| | ||||| | | || || ||||||| ||||||||||||||||||||||||||||||||| ||| ||||| | |||||||||||||||||||||||||||||||| || ||| ||||||||
-tctatgcatgtcattctgtttatgtttgcata-catttgtgtcaggtttaagctcacgattattgttgtttctcttattctaatgtacttatttgttttagGGATTCACCCATGGATTATGATGACAATGATTTTCAAAACCAGAATCTCCATTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCAGTATTAAGGCCATAT
upper sequence: Vv00s0229g00110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G17330.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------ctctccatccctctttccctctatgtttgtctctcacacatgcaagtgcatggatgtacccatgcaaatttctcctcatcta-acctttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
|| | | ||| | | | | |||| || ||| | | | || | | || | | | | || ||| ||| || ||||||||||||||||| ||| ||||||| ||| ||||| | ||||||||||||| | ||||||||| || |||||| ||| |||
gtagcgtctccatacactcttgtgtcggtacttttcgctttcctactgttttactccactcgacaagaaaatgaccagagtcgcttctttaaatatgtttcacggttgttgtgttatgcttttgtttcttttggttgtttgatgtttatatatgtctctgatttcagGAATAAACTCATGGATTATGATGACAGTGACTTTCAAAACCAGAATCTCCATTTAGCTGGTGAAGCCAACAACAAATTTCCACCAGTTTTACAGCCTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcatggatgtacccatgcaaatttctcctcatctaacctttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
atctaac putative branch site (score: 2)
tttctcctcatctaac CT-rich tract
aaatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctccatccctctttccctctatgtttgtctctcacacatgcaagtgcatggatgtacccatgcaaatttctcctcatctaacctttgcttccttgtagGGATACACCCATGGATTATGATGACAATGATTTTCAAAGCCAAAATCTTCGGTTAGCTGGTGAAGGGAGTGCCAAATTTCCTCCTGTTTTAGGGCCATAT
- - ccatccc
- - - - - - ctttccc
- - - - - - - - - - - - - - - ctctcac
- - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - -gcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttgc