Sequence
atgc intronic sequence ATGC exonic sequencegttaaataatacacattatgattattgattacacattctagaaaaaaagagacttaaattattaatgaaaatggacagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G21540.2 (Glycine max), 3'ss of exon 3
------------------------------------------------------gttaa--ataatacacattatgattattgattacacattctagaaaaaaagagact----taaattattaatgaaaatgga-cagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
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gtatgctccaaccccatcattttacttaacaaaattattcttcatacataataaattaataataatgttgataaagaataacgataaatgatgatgaacaagagttaattaaaataaatgactggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGACATAAACTTAATGAGTTTGAGCCTAGAAAAACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------gttaaataatacacattatgattattgattacacattctagaaaaaaagag-------acttaaattattaatgaaaatgga-cagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
| |||||| || |||| | | || | | || | || ||||| | ||||| ||| | ||| | ||||| | ||| | | ||||||||||||||| | | | |||||||||||| || || ||||||||||| |||||||| |||||||||||||||| |
gtatgctccaaccccatcattttactgagaaaattattcttcatacaaaagaaattaataatgatgatgatgaagaataatgaaaaatgatgatgaacaagagttaattaaaataaataattggttttgatgaaacagGTAAAAGGAGAAATCACATACAATGGGCATAAACTTAATGAGTTTGTGCCAAGAAAGACTTCAGCATACATTAGCCAAAATGATGTTCATGTTGGAGAAA
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------gttaaataatacacattatgat----tattgattacacattctagaaaaaaagagacttaaattattaatgaaaatggacagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
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gtcagttttcatattttgcatgggctcacatcttacaaaaaattagcttgtttggtaagtctaaaagtatataatatgatataatattaattactcatcttataatagtaa----ttaatttgc--atggaa-----cagGTCAGAGGGGAAGTGACTTATAATGGCCATAGGCTCAATGAATTTGTGCCACAGAAGACATCGGCATACATTAGCCAAAATGATGTTCACATAGGAGAAA
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g03550.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------gttaaataatacacattatgat----tattgattacacattctagaaaaaaagagacttaaattattaatgaaaatggacagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
|| || | || | | |||||| |||| ||||| ||| || || | | |||| || ||| || ||||| | |||| ||| || || ||||||||| | | | || |||||||||||||| ||||| |||||||| |||||||| |||||||| | |||| |
gtcagttttcatattttgcatgggctcacatcttataaaaaattagcttgtttggtaagtctaaaagtatataatatgatataatattaattactcatcttataatactaa----ttaatttgc--atggaa-----cagGTCAGAGGGGAAGTGACTTATAATGGGCATAGGCTAAATGAATTTGTGCCACAGAAGACATCGGCATACATTAGCCAAAATGATGTTCACATAGGAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgattacacattctagaaaaaaagagacttaaattattaatgaaaatggacagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
tattaat putative branch site (score: 2)
tagaaaaaaagagact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaataatacacattatgattattgattacacattctagaaaaaaagagacttaaattattaatgaaaatggacagGTGACAGGGAGAGTAACATACAATGGGCATGGATTGGAAGAGTTTGTGCCACAGAAAACATCAGCATACATAAGCCAAAACGATGTTCATGTTGGAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG