Sequence
atgc intronic sequence ATGC exonic sequencegtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G25060.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 7
----gtgttttttc-ttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
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gttggcattctccaatgcgcttgttttgtttatacataaggttaact-----ttacatcatgattaacttgatggttgcattatattatatgacagGTGGACGAGAATTTTCTTATGAGGACATTTGGTCGTTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTCGAACAGAAGAGGAACGCAGAAGGCAAA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
|| ||| || | | || |||| | | |||||| | | | || || | || |||| | ||||| ||||||||||| ||| || | || || || | ||||| || || ||||||||||||||||||||||| |||||||| ||||| || | ||||
----------gttgctttctctgct---gtgcggtttcattaaac--ttgtatgcgttgtcttgttagctttacatgctatggtgt--tagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 7
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
||| || | | | || | | ||| | || ||||| || ||| || | | | ||| | ||| ||| ||||||||||| ||| || | || || || | ||||| || || ||||||||||||||||||||||| |||||||| ||||| || | ||||
--gttgctttctctgctgtgcggttta---gttaaacttgtatgc-attgtcttgttagc-tttacatgctatggtgtta----------gGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggt-ataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
|| | | | | ||| | | | |||| | ||| | || || | | | |||| | | |||||||||||| ||||| ||||| || ||||| ||||||||||| || || |||||||| ||||||||||||||||||||||| ||||||| ||||| ||||
--gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaatt--gtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggta-taattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
||| | | | | || | | | |||| | | ||| | | || || | | | |||| | | |||||||||||| ||||| ||||| || ||||| ||||||||||| || || |||||||| ||||||||||||||||| ||||| ||||||| ||||| ||||
--gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaatt--gtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 6
---gtgttttttcttttcttac-ttggatcatatgttgttttctctcgccattgtattctt-------aatattcataaggtataat----tttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
| || | |||| | | || | |||| || | | | | | | |||| | | | || |||||| ||| | ||||| ||||||||||||||| |||| ||||| ||||||||||| || || |||||||| || || |||||||| || ||||| ||||| |||||||||||
gttgcattcctaatttttggatgctcaattctctgttattcttttactctttaatgctctttggacctgaaaccaacaaaatataatctgtttttattttttatagGTGGATGAGAATTTCCTTTTGCGTACTTTTGGAAGATTTGGTCCTATCGCTAGTGTGAAAATAATGTGGCCTAGGACAGAAGAGGAACGGAGGCGACAAA
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S196_109V6.1 (Physcomitrella patens), 3'ss of exon 6
------------gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtat-tcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
| || || | | | | |||| || | | | | | || || | | ||| ||||| | ||| | | || | |||||||||| || || |||||| | ||||| ||| |||||||||| || || ||||| || || ||||||||||| |||||||| ||| ||||| ||
tctcctcttgtagcgtgttgtttagtggtggttggtacagggactagtatgtgccttcaatgactatattactattc-tgaggggagctaatgtggtt---cagGTTGATGAAAACTTTCTTCTGAGAACTTTTGGACGATTTGGGCCTATCGCCAGTGTAAAAATCATGTGGCCAAGGACAGATGAAGAGCGCAGGCGGCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
tgctcac putative branch site (score: 2)
attgtattcttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG