Sequence
atgc intronic sequence ATGC exonic sequencegtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattagacgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19990.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
gtacacttgaatcttaaaccttcttctccatattgtgatgatgctaag--tggattagacgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
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gta-gttttagttgtag---tattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttata---acagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 4
-------gtacacttgaatcttaaaccttctt-ctccatattg-tgatgatgctaagtggattagacgtaatctcatctctc-------tgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
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atgagttgtttcgtcgattttgtagtcatcggattccatgtcaacaacagaattgattggataaattttaaaatgatctgccacaaaactttgtctgcagGGGGTTTTGTTGTACGGCCCTCCTGGAACTGGAAAGACGCTTCTTGCCCGGGCTGTAGCTCATCACACAGACTGTACGTTCATCCGAGTTTCAGGATCTG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 3
gtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattag-acgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
| ||| || | | | | | || ||| | | || | || ||| ||| |||| || | |||| ||| | | || || || ||||||||||| ||||| | |||||||||| || || || || ||||||||||| |||||||||||||| || ||||
------------gtaaaattttgctaacaaaagtttg-----gcttttggtaccagcatctattcttgtct-tctg-ctgtgcagGGAGTGCTACTGTATGGCCCTCCTGGAACTGGAAAGACTTTGCTGGCTCGGGCCGTGGCTCACCATACTGACTGTACATTCATAAGAGTTTCAGGGTCCG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 4
gtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattag-acgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
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------------gtaaaattttgctagcaaaagtttg-----gcttttggtaccagcatctattcttatct-tctg-ctgtgcagGGAGTGCTACTGTATGGCCCTCCTGGAACTGGAAAAACTTTGCTGGCTCGGGCCGTGGCTCACCATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGMapped 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|301502412|gb|HO207952.1|HO207952EST: CAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG GGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGG
genomic: CAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttga ... gtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgtgatgatgctaagtggattagacgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
tctcatctctctgtct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattagacgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT