Sequence
atgc intronic sequence ATGC exonic sequencegtcaggtttttagaaattggaattttaaactttacttttagaggaaaattgtttatatactcttacgttttctgaatgtcagtctcaaatatcttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39280.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 9
-------gtcaggtttttagaaattggaattttaaactttacttttagaggaaaattgtttatat---------actcttacg---ttttctgaatgtcagtct---caaatatcttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG
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gtcaggttttatgttctatctatttagtagtgtagcctagtcttacttcacaaagttgccaatgtgaaatgagcatttgtacgctattgtttgagcttccttctgatccattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
------------gtcaggtttttagaaattggaattttaaactttacttttagag----gaaaattgtttatatactcttacg---ttttctgaatgtcagtctcaaatatc----ttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG
|| | | | || | | ||| || | | || || | | | | ||| || | || || ||| | ||| || ||||| | ||||||| ||||||||||||||||||| ||||||||||| || || ||||| || ||||| ||| | || || ||||| | ||||
gtcaggttttatgttctatctattgagtagcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttgg-acttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------------------gtcaggtttttagaaattggaatt------ttaaactt--tacttttagaggaa-aattgtttatatactcttacgttttctgaatgtcagtctcaaatatcttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG
| | ||| | | || ||| ||| | | | | | | |||| | ||| | | | || | | | | || ||| | | |||||||| | || |||||||||||||| ||||||||||| ||||| ||||| || | ||||||||| || |||||||| || ||||
gtcagtctccatcatggcttatatagaaattagatgttatttggggcctacattgcatttaaaatctatttatatttctttgatttatggccatctcactaatcttagcattctcattgtcatgattgcattcataatgtcttggttacaagcttatgggttttgatggctttctcctgacttcagTTCTCCGGGTCTGGGATGTGCTTCTTTTTGAAGGAAACCGTGTCATGCTATTTAAAACAGCACTTGCTTTGATGGAGTTATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatactcttacgttttctgaatgtcagtctcaaatatcttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG
ctcttac putative branch site (score: 3)
tcttctttg putative PPT
aaatatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaggtttttagaaattggaattttaaactttacttttagaggaaaattgtttatatactcttacgttttctgaatgtcagtctcaaatatcttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA