Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28310.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 10
--------gtaagtctctctttgaaacgttctctttagagcaactcaaga------gtgtttagtcattgtca----gtactgagttttctgaaaaaaatt-ccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
|| ||||| | | || ||| || || | ||| | | || | | || | | | | || | | ||| | | ||| ||||||||||||||||| || || || ||| |||| |||||| ||||||| |||||||||||||||
gtatgtgattatttctctgtcctgagttttgtctacagtacatcccaatatgtatggcgtgaaagtgctatccacttgagttaggctaactaatctatattgctgttgttcagCTTTGTTGAAATAATGGCTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 10
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
| || | | | ||| | | ||| | || | | ||| | | | | | | || | | |||| ||||||||||||||||| || || || || |||| |||||| ||||||| |||||||||||||||
----------gtatgtagcttcctcct-----ctactt--gggtagctgatgtatgtgaaga--ggggctaactatttgtgtttgatgt-acagCTTTGTTGAAATAATGGCCCCGGTGTTCTCCAGAGATGCATGGAGATGTGTATGGCATATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 9
-------gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
| || | | | || | ||| ||||| | || | | ||| | | | | | | | ||| ||||||||||| ||||| |||| || ||| | || |||||||| ||||| |||||||||||||||
acatgaaggaaaaacagcaacggcataacaaaacggaaggaggatcaga-tgttttctttttcttaaaactatccgtcttcacattctgtttcacatgcagATTTGTTGAAATTATGGCAACTGTGTTCTCTAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 10
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgttta----gtcattgtcagt--actgagttttctgaaaaaaatt-------ccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
||| || | | ||| || ||| || || | ||| | | ||||| | | | || || || | || | |||| ||||||||||||||||| || || || || |||| |||||| |||||||||||||||||||||||
gtatgtgtttttttt---tcctcctcccagaaca-cttaccagttcccataatactaccatcagtctcccatacatacagaggcaacttatgtatgctctattacagTTTTGTTGAAATAATGGCTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G801369_T03 (Zea mays), 3'ss of exon 10
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
| | | | || || ||| | ||| | || | | | ||| ||| | | | | || ||||||||||||||| ||||| ||||||| || | || |||||||| ||||| |||||||||||||||
-----------gtaggagtgcaatcattta-------ttagattattttcttatcgaaatttctg---tttttcacatgtaatctgatatgcagGTTTGTTGAAATTATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
------------------gtaagtctctctttgaaacgttctctt--tagagcaact--caagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcac---agGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
|| ||||| | | | || || | || | | ||| | | | || ||||| |||| |||| || | | || | | | || ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||| |||||||||
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtc--tacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 10
--------------------gtaagtctctctttgaaacgttctcttt--agagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctca---cagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
|| ||||| | | | || | | || | || ||| | | || |||| |||| || | | || | | | || ||||| ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||||
gtatgctctctctcttccaccctggttcaaagttgaattgatgtattgcaatatcatttacctagattttcttttctttctctacttagttaactttactatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAGGCTTGGCGTTGTGTGTGGCACATGATTCAG
upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------------------------------------------------------gtaagtctctct-ttgaaacgttctc--tttagagcaactcaagagtgtttagtc----attgtcagtactgagttttctgaaa---aaaattccctct-----cacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
|||| | | || ||| || ||| | || | || || | | ||| || || ||| | | | || || ||| ||||| ||||| ||||| ||||| || ||||| ||||| ||||| |||||||||||||||||||||
gtatgctttctctctgttctccctctcttgcatatctggtgtgcgtgaatttgtctttatgagtgttaaaacatgcataaacacaatgtaaaaataaatattcaaatatttgtaacatagggtaaatatgttgtcttgggacttgcattttctcccctctcccctcttaggcttacagttttctacattaattcagATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
ttccctctcac CT-rich tract
ttttctgaaaaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC