Sequence
atgc intronic sequence ATGC exonic sequencegtctctctttcatcttcttctttattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttgatagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25560.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
----------------gtctctctttcatcttcttctttattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttg---atagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
|| | ||| | |||| | | || ||| | ||| | | ||| | ||||| | | | |||| ||| || ||||||||||| |||||||| |||||||| |||||||| || ||||| ||||| |||||||| | | | | || | | ||||| ||||| ||
gctggtaataaacaaagtgttatagtcaaaccatcaggtatt--tatataattttttaaa---aattttacctgaca-ctgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
------------gtctctctttcatcttcttctttattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttg---atagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
| | || || | || | || | || | | | ||||||| | | | ||||| | ||| || ||||||||||| |||||||| |||||||| |||||||| || ||||| ||||| |||||||| | | | || | | ||||| ||||| ||
agctggtaataaacaaaagtgttatagtcaacc--atcgggcatttatatcattttttaaatttttacctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G25590.1 (Glycine max), 3'ss of exon 1
---------------gtctctctttcatcttcttctt-tattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttgatagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
| | | | | | ||| | | | | ||||| || || | | ||| ||| ||| | | |||| | |||| || ||||| |||||||||||||||||| |||| |||||||| ||| | || ||||| || ||||| | || | || | | || |||| || ||
actttttattattccttatttatgtagtattcatatcatgtgagtttgtatttatttgatttgatgttgagttgctaactaactac---acttaaatatctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g00050.t01 (Vitis vinifera), 3'ss of exon 1
-------------gtctctctttcatcttcttctttattagttttta-gtttctcaaac-tgagtcaactttgataatt-gttgttgggatttaatttgatagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
| | | || ||| || || | | | ||| || | | | | | | ||||| || | ||| | | | | ||| || ||||||||||| ||||||||||||||||| |||||||| ||| |||||||||| ||||| | | ||| ||| || || |||||||| ||
atgttcttttagtgccattgttgcatgttacataccatatgatcacatgttggtctagcattaatatgccttgattctttgaccttgtggtgca---ttgcagGTTTGCAAAGGAATGGAAAGAGCTGCAGATTAAGGTGGATTAACTACTTAAGACCAGGATTAAAACGCGGGATGTTTACGATCGAGGAGGAAGAGACGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttctcaaactgagtcaactttgataattgttgttgggatttaatttgatagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
atttaat putative branch site (score: 4)
atttaatttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctctttcatcttcttctttattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttgatagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA