Sequence
atgc intronic sequence ATGC exonic sequence...gaaaattaaaaatagtgtctctcaacagtcactactgcatctttgttaatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08415.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 2
gaaaattaaaaatagtgtctctcaacagtcactactgcatc--tttgtt-aatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
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-----------gtacgatccaccgacgattattgcattattggcatgttgagatgataatgcaaaagactttagaaccgatgcttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 2
gaaaattaaaaatagtg--tctctcaacagtcactactgcatctttgttaatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
|| ||| || | | ||| | || | | | | || | | | | | | ||| || || || | | ||||| |||||| || || || || || | || || || || ||||| ||| | |||||||| |||||||| |||||||| |||||||||||||||||||||
acaagttacaatgcctagattgatcatgggcatatattttgtgctgctaaaactttattagatct--cattccctgttaattacaagctaccttttttgcagCGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G42600.1 (Glycine max), 3'ss of exon 4
gaaaattaaaaatagtg--tctctcaacagtcactactgcatctttgttaatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
|| ||| || | | | ||| | || || | | | || | | | | | | ||| ||||| || | | || || ||||||||| || || || || | || || || || ||||| ||| | |||||||| |||||||| |||||||| |||||||||||||||||||||
acaagttacaatgcctagatttatcatgggcatatattgtgtgctactaaaactttattagatct--cattccctgctaattacaagctaccatttttgcagTGTGGA-TATATTGTCCTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 3'ss of exon 2
-----gaaaattaaaaatagtgtctctca---acagtcactactgcatctttgttaatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
| ||| | | || | | | ||| | | || ||| ||| | || | || || || | | |||||| |||||| ||| || ||||| || ||||| ||| | || || || || ||||| ||| | ||||||||||||||||| |||||||| | |||||| || |||||||||
tatgcgtgttttagacaagatgcatatgatctacaaattttttggtatgtttatta-tacttgcttggaaaattataaga----attttg-attttcattt--tgtagTGTGGATTACATTGTTCTAACAAGTGTTGATCGTGATGATCTGCCTGATGGTGGAAGTGGCCATTTTGCTCGGACTGTTAAGGCTATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
tgttaat putative branch site (score: 3)
ttttgcattttccttt putative PPT
tatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaattaaaaatagtgtctctcaacagtcactactgcatctttgttaatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - -aaaaata
- - - - - - - - - - ctcaaca