Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaacttgttcactttgtttcattgatccaatgtggtgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25500.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g36960.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------gtgagttttcttttgtgcact-cttttagtcacccaa-aaaattacatgaccaa----cttgttc-actttgtttcattgatccaatgtggtg---ttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
| ||| | | | | || |||||| || | | | | || | | |||| | |||| ||||| | | | ||||||| || || | || || |||||||| || || ||||||||||||||||| | |||||| ||||| || ||||||||||||||| ||||||| |
gtaagttcttatggtcatgcaaaatctaattgaaatttacaaggaaacaaggatttctcttactggacaaattcaatagaatattgctaggagtcacacagcaggacttctctactatgacccctgttggatcatgttgagttgattgatttttccccctttcagGTTGGGGTAACTGTTGTAGTTGTCGAAAGTGCAGTTACATCGATATACATATGCTATGCTGAGGATCCCCGTTTAATTCAGAGATGGGATCCTGATTTTT
upper sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G801651_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------gtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaacttgttcactttgtttcattgatccaatgtggtgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
| | | | | | || ||| || | | | || ||| | ||| | | |||| | | ||||| || || | ||||| || ||||| ||||| ||||| ||||||||||| | ||| || ||||| | |||||||||||||||||| | || || |
gtaagtgccaatatctcgatatgaatttgcatgactagtaactaaggaaaggaaaaccgtgtccaagttttctttctcatacagtacaatctctgctagttctgtcaagattga--cgtctgctcaattttg----cagGTTGGACTAACTGTTGTGGTTGTGGAAAGTGCTGTTACATCAATATACATATGCTATGCCGAGGATCCCCTTTTGATTCAGAGATGGGATCCCGAATTTT
upper sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G21270.3 (Glycine max), 3'ss of exon 4
-----gtgagttttcttt-tgtgcactcttttagtcacccaaaaaattacatgaccaacttgtt----cactttgtttcattgatccaatgtggtgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
|| ||||| | || | | || || | || || | |||| | | || ||| | |||| | ||||||| || | | ||||| || || ||||| ||||| ||||| ||||||||||||| ||| |||||||| || ||||||||||| ||||| |||| || |
atttagtatgttttttaagtgactgacaatgtgaatttgcatgaatgcatattacttatttgtgtgaatgcatatttgcatgaaatatatgtatt-ttcagGTTGGAGTTGCTATGGTTGTGGTGGAAAGTGCTGTTACATCCATATACATATGTTATGCAGAAGATCCCTTATTGATTCAGAGGTGGGACACTGAGTTTT
upper sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24760.1 (Glycine max), 3'ss of exon 6
gtgagttttcttttgtgcactctttta-gtcacccaaaaaattacatgaccaact------tgttcactttgtttcattga--tccaatgtgg---tgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
| || | ||| ||| | | |||| |||| || || | | | || | |||| |||| || ||| || | ||||||| || || | |||||| || || ||||| ||||| ||||| ||||| || || | ||||||||| || || ||||||||||||||||||||||| || |
---tcctgtcgtgtgttgactatgaaaagtcagtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatttgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
upper sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G42290.1 (Glycine max), 3'ss of exon 6
gtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaact---tgttcactttgttt---cat-tgatccaa----tgtggt-gttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
|| || | || ||| || ||||| |||| || || | |||| ||||| | ||| ||| || ||| | ||||||| || || | ||||| || || ||||| ||||| ||||| ||||| || || | ||| ||||| || || ||||||||||||||||||||||| || |
---tgtgttgagtcgttgactattaaagtcagtcaaagctgtatattgttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
upper sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g03220.t01 (Vitis vinifera), 3'ss of exon 6
------gtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaacttgttcact-ttgtttcattg-atccaatgtggtgtt-cagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
| ||| | || | || ||| | ||| | ||| | | || | || | || ||||| || ||||||| | | |||||| || || ||||| ||||| ||||| |||||||| || | ||| ||||| || || ||||| || |||||||||||||| ||||
actcttgggagatgactatatataacctcattattttgttggggtcttatgaagtttatttgatgcttattatgggatgggatggaatgtacaattgtagGTGGGACTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATACATTTGCTATGCAGAAGACCCCTTATTGATCCATAGATGGGATGCTGAGTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattacatgaccaacttgttcactttgtttcattgatccaatgtggtgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
cattgat putative branch site (score: 4)
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaacttgttcactttgtttcattgatccaatgtggtgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT