Sequence
atgc intronic sequence ATGC exonic sequencegtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03650.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
-------------------gtatagatagat-tagacaccgt-tttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttc---cagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
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tctttgagttttaattgttgagaaaatgcatatacatgcagGATATGTATGAATTTTAATGAATACTGGCATGAGAACCTCACATACTGTACTTATGCAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 16
-------------gtatagatagattagacaccgttttacattaaactcattattaaaa---------gttatgtgagcggtgttgttcgggttc---cagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
||| | ||| | | || | | ||||||| | | | || ||| ||| | | ||| ||||||||||||||||||||||| | ||||| || ||||| |||| |||||| | || ||||| || || ||||||||||||||| | || ||||| ||||
ctgttgatactcagtacatgcagaagtg-tagtattgtgctgtaaactctgtttcagaatagaacagaattacatgaacatctcaacttctcttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 16
----------------------gtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttc---cagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
| | | | || | | || | | | || | | | ||| || | || | || ||||||||||||||||||||||| | || ||||| ||||||||| || ||| | || ||||| || || || |||||||| ||||| || ||||| ||||
atttggcctttttcttccactattctttgaaaaatacatgtagaaacacggaacaataataaatggtaac-atgagaacctcactggttctatttatgcagGATATGTATGATTTCATGGCCCTCGATAGACCTTCAACTCCTACCATTGATCGTGGGATAGCATTACATAAGATGATTAGACTTATCACAATGGGTTTAG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 16
----------------------gtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgttcgggtt---ccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
||| | ||| | | || || | | | || | | ||| | | |||| | || | |||||||||||||| |||||||| ||||||||||||| |||||| |||| ||| | || ||||| ||||||||||||||||||||||| || ||||| | |
ctgtcaaattatatgaggacacttatgtttgctttata-agtgtattgctgcagtttgccatttgacatatattttactaatgttctgttggctgcgtcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACTCCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGCCTTG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 16
----------------------gtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgt-tcgg--gttccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
| | | ||| | | || || | | | || | | ||| | | |||| | | || | | |||||||||||||| |||||||| ||||||||||||| || ||| |||| ||| | || ||||| ||||||||||||||||||||||| || ||||| | |
ctgtcaaatcatttaaggacacttgtgtttgctttata-agtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 16
-------------------------------gtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
| | | || |||| | || ||| | | || || |||| | | | || || || |||||||||||||| |||||||| | || || ||| |||||||| ||| ||| | |||||||| || ||||||||||| || ||||| || ||||| ||||
tggtcaagatagttacagtgtgtttatgctaccaaaagtgcatatgacaggcctatatatt---ttgacattttaatcttatattatggaatttatt----tttcagGATATGTATGAATTCATGGCTTTGGATAGGCCAACAACTCCTGCTATAGATCGTGGAATAGCATTACACAAAATGATCAGACTTATTACCATGGGCTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
attaaactcattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA