Sequence
atgc intronic sequence ATGC exonic sequencegttggtatttgaaattccacttacccagcaaaaaacagcatgtagtgactgtgtttagacttgattttaagctgacgttactttctttacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11910.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 9
---------gttggtatttgaaat-tccacttacccagcaaaaaacagcatgtagtgactgtgttta-gacttgattttaagctgacgttactttctttacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
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aattaagtaattaacgtgatatctatcctcttatttctcatataataat-tatggaaagttcagcaacaaatcgttgattgattaacgtccaattct--gcagATTAATGACCGGTATGAGTTCCCACTTCAACTTGATCTTGACAGAGATGATGGGAAATATCTTGCTCCTGATGCAGATAGAAGCATTAGAAACCTTTACA
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 9
------------------gttggtatttgaa-attccacttacccagcaaaaaacagcatgtagtgactgtgtttagacttgattttaagctgacgttactttctt-tacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
|| || | || | | | | | | |||| | | ||| | |||| | ||| ||| | ||| | ||||||||||| || |||||||| ||||| ||||| ||||| || ||||| |||||| |||| |||| || |||||||| ||| | | || ||||| |
gttagaaccgtgctgaataccaccatccaaatgataaaccacttccatacatcttaagaaatggtgaataaggttacccaggattg-gtgatgatcttatctacttctgcagATTAATGACCGCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATA
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------gttggtatttgaa---attccacttacccagcaaaaaacagcatgtagtgactgtgtttagacttgattttaag--ctgacgttactttctt-tacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
||| | | || | ||| || | | | | ||| | | || || | || ||||| | | || ||||| ||| |||||||||||||| |||||||| ||||| ||||| ||||| || ||||| | ||| | ||| | | || ||||||| ||| || || || ||||
gtttgttctgataacttgcacttcgttcagttagttatattgttcatgtactttagggtacacttgattgatttgtgcagtaattacaatcaatctaaatcaaatatattttaacacctattctttattgtgattgtcatgtctattaatacttgcttgcccagATTAATGATCGCTATGAGTTCCCTCTGCAACTTGATCTGGATAGAGATGGTGGCAAATACATTGCTCCAAATGCAGATCGAAGTACACGAAACCTTTACA
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------------gttggtatttgaaattccacttacccagcaaaaaacagcatgtagtgactgtgtttagacttgattttaagctgacgttactttctt--tacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
|| || | || | | || | | | ||||| ||| | |||| ||||| || ||| || | | |||||||||||||| |||||||||||||| ||||| || || || ||||| |||||| |||| | || |||||||| ||| ||||| || ||| | ||||
gtgaggaaaggggttttcgaaccatgcaatatgcaacattcggctggtatagcttatgtattgattgtgcatattatttagatgaaggacgtgtgtgtgtgtgtgtgtgtatttgctttgttttggttggttggtagtcact-tttttactactgattacctttgaacattatttatgtgatgcagATTAATGATCGCTATGAGTTTCCTCTGCAACTAGACCTGGATAGAGAGAATGGAAAATATCTCTCTCCTGATGCTGACCGCAGTGTGCGAAATTTATACAMapped 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|164142494|gb|ES202896.1|ES202896EST: GAGGGACACAATGGTGAAG ATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGAT
genomic: GAGGGACACAATGGTGAAGgttggtattt ... ttctttacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgtagtgactgtgtttagacttgattttaagctgacgttactttctttacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
agctgac putative branch site (score: 3)
ttactttcttt CT-rich tract
ttgattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtatttgaaattccacttacccagcaaaaaacagcatgtagtgactgtgtttagacttgattttaagctgacgttactttctttacagATTAATGATCGGTATGAGTTTCCTCTCCAACTGGATCTCGACAGAGAAGATGGAAGATATTTATCCCCTGATGCAGACAAGAGTGTCCGCAATCTCTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA