Sequence
atgc intronic sequence ATGC exonic sequencegtaatggtactcttttgtcttcttcattatttaattttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaagtagagggatgtgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65930.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 17
---gtaatggtactcttttgtcttcttcattatttaattttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaa-gtagagggatgtgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
|||| | | ||| | | ||| | | | || | | ||| ||| | |||||| ||| | || | || | || | || || | |||||| || |||||||| ||||| |||||||||||||| ||||||||||||| || ||| | ||||| | |||| |||||||||||||||||| |||||||
gttttaatacttttatttcattattatcactgctccaattgtataatagccaaat-atgtttcaatattttgtttatttttactttattgtgaaatttaaaacatatgagcatgctttatgat-ttagGATATCGACAGAAAGAATGAACAAACAGCTGCCATACTGAAAATGCAAGGGGCTCAATTAGCTGAAATGGAAACACTTTATAAGGAAGAACAGGTTTTAA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 17
gtaatggtactcttttgtcttcttcattatttaattttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaagt-agagggatgtgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
||| | |||| || | | || |||| || | ||| || ||| ||| | | |||| | | | | | | || ||| | |||| || ||||||||||||||||| |||||||||||||||||||| |||| ||||||| || ||||| ||||| | ||| | |||||||||||||| || ||| | |
----------gttttgatactcttatttttatcatcacttttcggtcagcatgctg----tgtgcattcaccttaggtgtatgaatttaaaaaaaaatttataaatttctatttgcttcatgtagGACATTGACAGAAAGAATGAGCAAACAGCTGCCATACTGAAGATGCAAGCAGTTCAACTAGCTGAAATGGAATTGCTTTATAAGGAAGAGCAGGTTCTCA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 17
gtaatggtactcttttgtcttcttcattatttaattttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaagtagagggatg-tgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
||| | |||| || | | || |||| || | ||| | |||| || | | |||| | | || | | || ||| | |||| || ||||||||||| ||||| |||||||||||||||||||| |||| ||||||| || ||||| ||||| | ||| | |||||||||||||| || ||| | |
----------gttttgatactcttatttttattatcacttttcggtcagcatgct----atgtgcatttaccttaggtgtatgaatttcaaaaataatttataaatttctatttgcttcatgtagGACATTGATAGAAAGAATGAGCAAACAGCTGCCATACTGAAGATGCAAGCAGTTCAACTAGCTGAAATGGAATTGCTTTATAAGGAAGAGCAGGTTCTCA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 20
gtaatggtactc---ttttgtcttcttcattatttaattttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaagtagagggatgtgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
||| | |||| ||| | | || | | || | || | | ||| | | | | ||||| ||| | || | | | | | | ||| || | |||||| || || ||||| ||||| || ||||||||||| ||||||| ||||| || ||| | ||||| | ||| |||||||||||||||||| |||||||
gtattaatacttatatttcattattttaactgcttcaattgtatagtagccaaatagttttt-tatgttttctttattttcacttta--ttgtgaatttaaaacatgaatgtgttttatgat-ttagGATATCGATAGAAAGAATGAACAGACAGCTGCCATACTGAAAATACAAGGGGCTCAATTAGCTGAAATGGAATCACTTTATAAGGAAGAACAGGTTTTAA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 16
gtaatggtactcttttg--tcttcttcattatttaa--ttttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattga--agtagagggatgtgtttacattccaattt----cattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
||||| | || | || | ||| | || ||| | | || || | ||| | | | |||| |||| | |||| | | | | | ||| | | || |||| | | | | |||||||||| ||||| ||||||||||| || || || ||||||||||||| || || || |||||||| ||| | ||||| ||||| ||||||||| |||
gtaataatcctatactggattttcatttttgttttaactgttcattatatttttaggttagtaat--atttctgtttctcaatactcataaattgagaacctttctaactaataaattcttggcttgctttcagGACATTGATAGAAAGAATGAGCAAACTGCCGCTATCTTGAAAATGCAAGCTGCTCAGCTAGCTGAGCTGGAAGTTCTTTACAAGGACGAACAAGTTCTAA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 17
--------------------------------------------------------------------gtaatggtactcttttgtcttcttcattatttaa--ttttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaagtagagggatgtgtttacatt--ccaatttcattttc----ttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
|| || || || ||| || || || || | |||| | || |||| | || |||| | | | |||| || | | |||| || |||| ||||| |||||||||||||||||| |||||||||||||| || || ||||| || | || ||| | |||| ||||||| | || | ||||||||||| |
gtagagaaaaaaacatgtatctaggatgaaaatgcatggttgacatgactattgatatatttttttttgttattgtgacctattgaaatcatcgtttattgagtttttataactacttgagttgtgtaggattattaactttgaaagataatgaattatgattacttttttattttattttattttatttttgtttttagGACATTGACAGAAAGAATGAGCAAACAGCAGCTATATTGAAGCGACAGGCAGACCAGATAACTGAACTAGAAACGTTGTACAGAGAAGAACAAGTCCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgattcaaaattgaagtagagggatgtgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
tttcattttctt CT-rich tract
aatttcattttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggtactcttttgtcttcttcattatttaattttgtttctgtttgaatgatgataatgtattttcgcgattcaaaattgaagtagagggatgtgtttacattccaatttcattttcttagGACATTGACAGAAAAAATGAGCAAACAGCTGCCATTTTGAAAATGCAAGGAGCCCAACTTGCTGAGCTAGAAATACTTTATAAGGAAGAACAAGTTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC