Sequence
atgc intronic sequence ATGC exonic sequence...tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaatcaaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaat----caaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
|| || || || |||| | ||| |||| ||| | ||| || | ||| | | | | | ||| | || || ||||||||||||||||| || |||||||| ||||||||||| || || ||||||| ||||||| ||||| ||||||||||| || || |||||
-----------gtcagtgctgtttct--tcgtatc--attgcttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 6
tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaatcaaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
|| | || | |||| | || | | | | | | | ||| | || | | | ||| | | || || || ||||||||||||||||| || |||||||| ||||||||||| || || ||||||| | ||||| |||||||||||||||||||| || |||||
-----------gtaagtgatgtttcagatcattacagatacatgattttgttgattgtgttttatttatttattt----ctatattttggctctc---agAGATATAAACATGATGATGGTGGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGC
upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 6
tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaatcaaatttttacatcttaataaaaccgaattcttgttc---cttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
|| | || | |||| |||| | | | | || || || |||| | || || | | | | || | || || || ||||||||||||||||| || |||||||| ||||||||||| || || ||||||| | ||||| ||||| ||||||||||| || || |||||
-----------gtaagtgatgtttcagatcattgctgatacatgatttaattaa--taatgctttatttattcatccattcatttctatattttggcatacagAGATATAAACATGATGATGGTGGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCTGTCATGAACATTGCCCCTTTGGCTATCTCAACAACTGGC
upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
-----------------------------------------tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaa-----tcaaatttttacatcttaat--aaaaccg-aat---------tcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
| | | | | | | ||| | | || | | || || || || | || ||||||| || | | ||| ||||| | ||| ||||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| ||||| ||
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggta-ttattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctt-tagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 6
---------------------------------tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaa-----tcaaatttttacatcttaat--aaaaccg-aat---------tcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
| | | | | | | ||| ||| | || | | || || || || | || ||||||| || | | ||| ||||| | ||| ||||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| || || ||
gttagagttttctcttgatctcctttctgttagttttttttgtcagctccttttctgttagtcgaagttggta-ttattgaaatccaagttggtctgctccttttctcttaatataagattgtaatgctagtctgtcttgcttctt-tagTGACATCAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACTACAGGC
upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 6
-----tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaatcaaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
|| | | | | | | | | | || || | | |||| || ||| ||| | | | ||| | ||| ||||| | || || ||||| ||||||||||||||||||||||| || |||||||| |||||||| | ||||| || ||||||||||| |||||||||||||| ||||| ||
gtaagtcttgcttgaaaacagatttcagattcgactcattggatactttttgtct--aactcatttttctttcttcacttgaaaacaaat-cttgtgcttt-cagAGACATCAACATGATGATGGTTGGTGATCCATCTGTTGCCAAATCTCAACTTCTGAGAGCGATAATGAATATTGCACCTTTGGCTATATCAACCACAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcataaaatcaaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
tcttaat putative branch site (score: 3)
ttcttgttccttat putative PPT
taaaatcaaattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaatcaaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- -ctcctcc
- - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa