Sequence
atgc intronic sequence ATGC exonic sequence...tcatcaatatatattgaaattgcctgacgcattttagcatgctatcaggcacttctggtgatttttgtctgttttttgctgtgcttgctgcttattgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 9
tcatcaatatatattgaaattgcctgacgcattttagcatg--ctatcaggcacttctggtgatttttgtctgttttttgctgtgcttgctgcttattgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
| | | || | || | | | ||| | | | | | || | ||||||| || |||| | | |||||||| |||||||||||||| || ||||||||||| |||| ||| | ||||| ||||| || || | | ||||| | ||||| |||
-tagaatcttgcatggcgtactactaattcttcctagaaaagcttggctagatatgcttttctgttttgtccccttacc-ctgttaagacaatacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG
upper sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
tcatcaatatatattgaaattgcctgacgcattttagcatgctatcaggcacttctggtgatttttgtctgtttt-ttgctgtg-cttgctgcttat--tgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
|| ||| | | || | || || | || ||| | ||||| |||| | | || | ||||| ||| |||| ||||||||||||||||||||||||||||||||||||||||||| |||| | |||||||||||| || || | ||||||| | ||||| |||
----acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
upper sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
tcatcaatatatattgaaattgcctgacgcatt-ttagcatgctatcaggcacttctggtgatttttgtctgttttttgctgtg-cttgctgcttat--tgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
| || | || || || | | ||| || || | | | | | | |||||| | | | | |||| ||| | |||| | |||||||||||||||||||||||||||||||||||||||| |||| | |||||||||||| || || | ||||||| | ||||| |||
-tgtaaacttcaataatgatcatttggcataccattatgatcctttgaagg--ctgtattaatttttttactctatct-ctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG
upper sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 9
tcatcaatatatattgaaattgcctgacgcatt-ttagcatgctatcaggcacttctggtgatttttgtctgttttttgctgtg-cttgctgcttat--tgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
| || | || || || | | ||| || || | | | | | | |||||| | | | | |||| ||| | |||| | |||||||||||||||||||||||||||||||||||||||| |||| | |||||||||||| || || | ||||||| | ||||
-tgtaaacttcaataatgatcatttggcataccattatgatcctttgaagg--ctgtattaatttttttactctatct-ctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTG-----
upper sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 6
---------------------tca--tcaatatatattga--aattgcctgacgcattttagcatgct--atcaggcacttctggtgatttttgtctgttttttgctgtgcttgctgcttattgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
||| | |||| | | | | || || | |||| | || || | | || | | |||| | || | || | ||| | || || ||||| |||||||||||||| || || | || || |||||||||| |||||||||||| |||||||| | ||||||| || ||| ||||
gtgagtaacagcttaaacccgtcaagttgatatgtctatatcagttatgcgagtccttttggtgcactgaattatactagtcagtttgattttatttgctaattatggagctcttttctgcgtgtagGACAAATTTGATGAAGCTCCGATCCCAATACAAGGATGCATTTTATGAAAAGCATGGAGTGAAGTTGGGGCTTATGTCTGGATTTATTAAA
upper sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------tcatcaa-tatatattgaaa---ttgcctgacgcattttagcatgctatcaggcacttctggtgatttttgtctgttttttgctgtgcttgctgctta--ttgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
|| || || || | ||| | | | | | ||| | |||| || |||| | |||| | || | || ||||||| || ||||| || | |||||| | |||| || | ||| | ||||||||||||||||| || |||||||||| |||||||| |||
gtaagtttctttcttgaaaattcttgctaagtagttgttcagatgaagcttagatccgagcccttgatttgttcttcctgttacagtattatctttttctaatg--ttttacatattttgaggctcagatgtttctgtgtttgcagGGGTAACCTGATGGAGTTGCGTTCTCAACATAAGGACACGTTTCTGGAAAAGCATGGTGTGAAACTAGGATTTATGTCTGGGTTTGTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggcacttctggtgatttttgtctgttttttgctgtgcttgctgcttattgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
tgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatcaatatatattgaaattgcctgacgcattttagcatgctatcaggcacttctggtgatttttgtctgttttttgctgtgcttgctgcttattgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG
tcatcaa
- - - - - - - - - - - cctgacg
- - - - - - - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - - - - - tcaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgct