Sequence
atgc intronic sequence ATGC exonic sequencegtaatagaattaaagcttgtttatcaagtaacctaacttgcttctcttctgttagtgaaggaactaagaatggattttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G22240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 6
--------------gtaatagaattaaagcttgtttatcaagtaacctaacttgcttctcttctgttagtgaaggaactaagaatggattttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
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gtatatatgtacatatgatgaactccaactcgggtgatc--gcgatcgatgaaacatgaattggtttgttgtgcatatggaaattgg---caatggcagCCGACGTCGATCGCGAGCTACAACCACCTAGGCAACAACGACGGCATGAACCTGTCGGCGCCGCAGACGTTCCGGTCCAAGGAGATCTCCAAGAGCGGCG
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 6
gtaatagaattaaagcttgtttatcaagtaacctaactt-gcttctcttctgttagtgaaggaactaagaatggattttgtg---------gcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
|| |||| | || | | || || ||| | || || || | ||| | ||| | ||| |||||| || |||||||||||||| || || ||||||||||||||||| |||||||| || || || || || ||| | || |||||||| || |||||||| |
---gtacaatttatcaatgaa-acctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 2
gtaatagaattaaagcttgtttatcaagtaacctaactt-gcttctcttctgttagtgaaggaactaagaatggattttgtg---------gcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
|| |||| | || | | || || ||| | || || || ||| | ||| | |||| |||||| || |||||||||||||| || || |||||||||||| |||| |||||||| || || || || || ||| | || |||||||| || |||||||| |
---gtacaatttatcaatgaa-acctgatatccccccttcgaaatgtttttggcagacgtcatacttacaataattcttgtatatgttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACAACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
-----gtaatagaattaaagcttgtttat-caagtaacctaacttgcttctcttctgttagtgaaggaactaagaatggattttgtg---------gcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
| | || | | ||| |||| || | | | | | ||| | ||| |||| |||||| || |||||||||||||| || || |||||||||||||||| |||||||| || || || || || ||| | || |||||||| || |||||||| |
cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------------gtaatagaattaaagcttgttta---tcaagtaacctaacttgcttctcttctgttagtgaaggaactaag------aatggattttgtgg-------cagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
| || ||||| || ||| | || ||| ||| || || || | | |||| || | ||| | || ||| ||||| || || || ||||| || || |||||||||||||| || || ||||| |||||||| || || || |||||||| ||||| ||||| ||||||||||
gtacaacttttgttgttttgcttactaatactattgctatatcacgtgtgctactacttttattggttaataataaggacagagtatcatttgtatgcttaaactttaattaaaataaaataaaataatgtg-ttggctaaaaatggagaagtaaattgatgttttaattgtcttggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATTTGGGAAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCGAAGGAAATTTCCAAGAGCAATG
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------gtaatagaattaaagcttgtttatcaagtaacctaacttgcttc---tcttctgttagtgaaggaactaagaatggattttg----tggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
| | |||| | || | | || ||| | || | | | | | | | | | | | | | ||| || || ||||| || || |||||||||||||| ||| ||||||||||||| || ||||| || || || || || || |||||||| |||||||| || ||||||||||
gtatatcatttttagcatttcctctgttgaaatttagaattttaaagtaaataagtatgcatgtataggattatgtatgaataatgatattgaaagatgatgatggtggtgacagCCAACATCCATTGTGAGCTATAACCATCTGGGAAACAACGATGGCATGAATCTGTCTGCTCCTCAAACCTTCCGCTCCAAGGAGATCTCCAAGAGCAATG
upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------gtaatagaattaaagcttgtttatcaagtaaccta--acttgcttctcttctgttagtgaaggaactaagaatggattttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
| || || | |||| || ||| ||| | | || | | || |||| ||| || ||||| || || ||||||||||| |||||||||||||||||||| || |||||| | ||||| || ||||| || || || |||||||| || || |||||||
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaatt-attgtgca-cagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86066779|gb|DR362536.1|DR362536EST: CTAAGATGAAATCCGTTTTGGTTGATTTCCATGTTGGAGCTGGCATTAAG CCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAAC
genomic: CTAAGATGAAATCCGTTTTGGTTGATTTCCTTGTTGGAGCTGGCATTAAGgtaatagaat ... tttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAAC
EST:
gi|86066778|gb|DR362535.1|DR362535EST: CTAAGATGAAATCCGTTTTGGTTGATTTCCTTGTTGGAGCTGGCATTAAG CCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAAC
genomic: CTAAGATGAAATCCGTTTTGGTTGATTTCCTTGTTGGAGCTGGCATTAAGgtaatagaat ... tttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctaacttgcttctcttctgttagtgaaggaactaagaatggattttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
acctaac putative branch site (score: 2)
taagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagaattaaagcttgtttatcaagtaacctaacttgcttctcttctgttagtgaaggaactaagaatggattttgtggcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA