Sequence
atgc intronic sequence ATGC exonic sequencegttgccttttctactggagatattgctgataagttcacacaccacatttcgtagaattacatttccttactgcaaaaccattttatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT5G08650.1 |
| intron # | 15 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 15
------------------------gttgcct-tttctactggagatattgctgataagttcacacaccacatttcgtaga-------attacatttccttactgcaaaaccattttatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
| ||| | || |||| |||| | | | | || ||| ||| | || | || | | | ||||||||| |||| ||||||||||| ||||||||| | | |||||||| ||||||| || ||||| || ||||| |||||||| | || | || | ||
gttgtatctgtgtacatgatgttcaccatcaatttgcagtgacattattattgatctttgggagtagtgtcatgcacaggcctggttattgtttttgatgtcttcctttccctcctttgcagATTGAAATGCTTACACCAAAAGATTATATTGGTTCAATAATGGAGCTGACTCAAGACAGAAGAGGTGAATTCAAGGAAATGAACTTCATCACAGAAAGCA
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 15
-------------------------------------------------gttgccttttctactggagatattg-ctgataagttcacacacc-acatttcgta---gaattacatttccttactgcaaaaccattt-tatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
| || ||| || | || || | | |||||| | | | | || | ||| ||| || || | || | |||||||||| |||| |||||||| ||||| |||||| | |||||||| || || ||||| || |||||| |||||||||||||||||| ||| ||||| || |
gttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaattttaattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 15
-------------------------------------------------gttgccttttctactggagatattg-ctgataagttcacacac---cacatttcgtagaattacatttccttactgcaaaacca-ttttatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
| || || || | || || | | | |||| | | | | | | || | || ||| || || | || | |||||||||| |||| |||||||| ||||| |||||| | |||||||| || || ||||| || |||||| |||||| ||||||||||| ||| ||||| || |
gttatttcttgcactttgttctgtttattgttcaccttgttcaagagttgaagcagttagggctaaacattttaattcacatgttctctctctctctctctctgtgtatttgtctttatttggaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTTCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAGAGAAATGAAATTTATTGCTGAAAATA
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 15
--------------------------------gttgcc-ttttctactggagatat-tgctgataagttcacacaccacatttcgtagaattacat-ttccttactgcaaaaccattttatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
| | | |||||| | | | | ||||||| || || |||| | | | || | ||| || | | |||||||||| ||||||| |||||||||||||| ||| | || ||||| | |||||||| | ||||| ||||||||||||||||||| ||| ||||||| |
gttgttgcctgcatctatagatgttctcccatttagtcattttctgatatatccagatatctttaagttcttgtttcaaatcctaaagaaaaaaaggctatttgattttaaaacaatatgtacagATTGAGATGCTCACTCCAAAAGACTATATCGGTCCTCTCATGGAATTGGCTCAAGACCGTAGAGGAGAGTTCAAAGAAATGAAATTTATCACTGAGAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacacaccacatttcgtagaattacatttccttactgcaaaaccattttatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
tccttac putative branch site (score: 2)
ccatttt putative PPT
aaaaccattttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgccttttctactggagatattgctgataagttcacacaccacatttcgtagaattacatttccttactgcaaaaccattttatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
