Sequence
atgc intronic sequence ATGC exonic sequencegttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23990.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gttagtccatgttataatgttt----tgggagtc---ttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagcta--attgtgttt-----agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
|| || ||||| ||| ||| || | | ||| || | | | || | || | || | | | | || ||| |||| |||||||| |||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||| || || |||||||||||| ||||||
------acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaa-gttatattttgacctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
---gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaa----ttgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
| | ||| ||| | || || ||| | | || | | | || || || | || | | || |||||||||| ||||| |||||||| || |||||||||||||| || |||||||| ||||| | ||||| || ||||| || || || ||||||||| ||||||
agtggcggaacattctattactattactgattctagtgactgtcctgagttgtgagcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
----------------------gttagtccatgttata----atgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaat---tgtgttt--------agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| ||| | | |||||| | || | | | ||| |||||| | || || | | |||| | ||||||| ||||| || ||||| ||||||||||||||||| || |||||||||||||| ||||||| |||||||| || ||||||||||||||| ||||||
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
-----------------------------------gttag--tccatgttataatgttttgggagtcttagaatcatagcagcctgg------ttgtaagtgtcttgttata-acttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
| ||| | |||||| | | || | || ||| | | |||| || | | || || | | | || | | |||||||||||||| || ||||| ||||||||||||||||| || |||||||||||||| ||||||| |||||||| || ||||||||||| ||| ||||||
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
-------gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgta-agtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
| || | | | | | | || | ||| | | |||| | | || | | |||| | || | || | | ||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| || ||||| ||||| || || || || || || ||| || |||
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaat-taacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
----gttagtccatgttataatgttttgggagt-----cttagaatcatagcagcctggttgta-agtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
| ||| || || || | | || | ||| || |||| | | || | | || | | | || | | ||||||||||||| |||||||||||||||||||||||||| || |||||||| ||||| || ||||| ||||| || || || || ||||| || | || |
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaat-tgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 13
gttagtccatgttataatgttttgggagtcttagaatcatagca---gcctggttgtaag----tgtcttgtta----taacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| || || | | | ||| | | | || || | || | | || | |||| || || |||| |||| | | | | ||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| || || ||||| || ||||||
gtttgtttatttgagtttaccttgcttgctgttaagtcttatctggtgcttcatcatatggttttgtcatgataaaattaacatctgaaaccttacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
gttagtccatgttataatgttttgggag-tcttagaatcatagcag---cctggttgtaag----tgtcttgttataact----tctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| || || | | | ||| | | |||| || || | | | | | || | |||| || || |||| |||| | | | | ||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| || || ||||| || |||| |
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------------------gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgttt--agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
| | || | || ||| ||| | || ||| |||| | | || | | | | | | | | || ||| |||| |||||||| ||||||||||||||| ||||||||||||| || || ||||||||| | ||||| ||||| ||||| || ||||| || ||| ||||||
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagctactgtactggta--ctcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------gttagtccatg--ttataatgttttggga----gtcttagaatcatagcagcctggttgt----aagtgtcttgttataacttc-tggagctaattgtg---------tttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| | | ||| | | |||| ||| ||| | | | | | ||| | || ||| || | || |||||| | | ||||| |||||| | ||||||| ||||| |||||| ||||| | || || ||||| |||||||||||||||||||| || |||||||| ||| |||| |
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
--------------------------gttagtccatgttataatg----ttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctg---gagctaatt---------gtgttta--gATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| | | | | |||| || | || || ||| | | | || ||| | | ||| || | || | ||| ||| ||| |||||||||||| ||||||| ||| ||| |||||||||||||| | || || ||||| ||||||||||| ||||| || ||||| ||||| ||| | || |
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------gttagtccatgttataatgttttgggagtcttagaat-catagcagcctggttgtaagtgtc-ttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
| | | | ||||| || | | || | || | | | ||| | | | || ||| || || ||| | | | ||||| |||||||| ||||||| || || |||||||||||| | || || ||||| ||||| ||||||||||| || ||||| ||||||||| | || |
gtatatccatgtacttcaattatctgtctcatttac-tcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGMapped 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|124764522|gb|EH854652.1|EH854652EST: CTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAG ATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAAGACAGAGTGAC
genomic: CTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccat ... ttgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAA-GACAGAGTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
ttgttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG