Sequence
atgc intronic sequence ATGC exonic sequence...acttttcttcatgatcgaatctatgttcttgctaagttttttgatttttttttcctgaagatggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 8
acttttcttcatgatcgaatctatgttcttgc-----taagttttttgattttt---ttttcctgaagatggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
|||| || | ||| | || | | | || || ||| | | | | |||| || | | ||||| | | | || |||||||||| ||||| || | | |||||||||||||| ||||| || ||| |||| ||||||||||||| ||||| || ||||||| || ||||| |||
-----tcttgataag-gaaaatgtgctttgacacatacaaattacttggtaatgaagtgactttttagattgtgtgcttcagaacattttcgtcctctctt--ttcagGATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAG
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 4
acttttcttcatgatcgaatctatgttcttgctaagtttt--ttgatttttttttcctgaagatggtttctcaagcca--tatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
|| || | || || || | || |||| | || | || |||| | | || | | ||| | | | || |||||||||| ||||| || | | ||||||||||| || |||||||| ||||||||| |||| |||||||| ||||| || ||||||| || ||| | |||
-taatttttttgggtca---ttaagtggtccctgagttctaatttaggaagcattaatgaacttaatacaaaaaagctgctgctttaaagattttttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTTCAGTTAAAACGGTTTGAATATGATTTTGTGCGGGATACGATGCTCAAG
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 8
acttttcttcatgatcgaatctatgttcttgctaa-gttttttgatttttttttcctgaagatggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
|| | | | || | | || || || || | | | || | | || | |||| || | || |||||||||| || || ||||| | || |||||||| ||||| ||||||||||| ||||| ||| ||||||| |||||||| ||| ||||||| |||||||||
-ctaagccaagttaattaaccaccgacctaactgttattattacaaatgcagtccccttatctagtcttaatctgggggaacttgatttctattgtttcagGATGCAAAAAAAGGTGTTCTTTTCATTGACTTTCCACCGGTTCTTCAACTCCAGCTCAAGAGGTTTGAATATGACTTTATGAGGGACACCATGGTGAAG
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
--acttttcttcatgatcgaatc-tatgttcttgctaagttttttgatttttttttcctgaagatggtttctcaagccatatttttgaattgtgttactt-cagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
| || || || | | || | | | || || || || ||||| | || | | ||| |||| | | ||| || |||||||| || || ||||| |||| || ||||| ||||||||||||||||||||||| ||| ||||||| || || || ||| ||||||| |||||||||
atatttcaaagcaggaacagctgataaagttgcatttgactaatttatattgttactctgaacttatcttatattggaatactttt----tttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
------acttttctt-----catgatcgaatctatgttcttgct----aagttttttgatttttttttcctgaag------atggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
| ||||| | | ||| | ||| | | | | | ||| | || | | | | | || || | ||||| || | || | || |||||||| || || || ||| ||||||| |||||||| || |||||||| || ||| ||||||| |||||||||||||| ||||| ||||| |||||||||
gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 8
------acttttcttcatgatcgaatctatgttcttgct--aagttttttgatttttttttcctgaagatggtttct-----caagccatattt--------ttgaattgtgt-tacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
| | || || | | | || |||| || ||| |||| || | || ||| ||| || | || || || || ||| || | | |||||||| || || || ||| ||||||| |||||||| || |||||||| || || || || |||||||| || ||||||||||| ||||| |||||||||
gtgctgaatgcgctgcaccttttgaatcaaattgatgcttgaactttactgatcttctgatcatgattatgaattgtatctgtaaaccctacttcaaccaatttggggcacgtacattgcagGATGCAAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTCCAACTGAAACGGTTTGAATACGACTTCATGCGAGACACAATGGTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttcctgaagatggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
ttacttc CT-rich tract
atatttttgaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttttcttcatgatcgaatctatgttcttgctaagttttttgatttttttttcctgaagatggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - -catgatc
- - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaagc