Sequence
atgc intronic sequence ATGC exonic sequence...atattctcttttttttttaaagaaacataaaatttctaatattttgaccttttgtaatgtaagaaatttatgacattaatatttagttttacatttgcagCGAGGTGTAAACTAGGGTATGAAGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71930.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
atattctcttttttttttaaagaaacataaaatttctaatattttgaccttttgtaatgtaagaaatttatgacattaatatttagttttacat-ttgcagCGAGGTGTAAA---CTAGGGTATGA------AGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC
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gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattg-ggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: AT1G71930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-----------------atattctcttttttttttaaagaaacataaaatttctaatattttgaccttttgtaatgtaagaaattta--tgacattaat--atttagttttacatttgcagCGAGGTGTAAACTAGGGTATGAAGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC
| ||| ||| ||| ||| | || | | || | || | ||||| | | || ||| || ||| |||| || ||| |||| | | || | | ||||| |||||||||||||||| || || || |||| ||| ||||| |||||||| ||||||||| ||||||| |
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttcta-aatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: AT1G71930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
------------------atattctcttttttttttaaagaaacataaaatttctaatattttgaccttttgtaatgtaagaaattta--tgacattaat--atttagttttacatttgcagCGAGGTGTAAACTAGGGTATGAAGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC
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gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttcta-aatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGGMapped 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|86053054|gb|DR348811.1|DR348811EST: TGTCATTGTAGAGATTGATCTCTACAAAATGGAGCCATGGGATATACAAG CGAGGTGTAAACTAGGDKTATGAAGAGCAAAACGAGTGGTACTTCTTTAGT
genomic: TGTCATTGTAGAGATTGATCTCTACAAAATGGAGCCATGGGATATACAAGgtaattatat ... acatttgcagCGAGGTGTAAACTAGGG-TATGAAGAGCAAAACGAGTGGTACTTCTTTAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaccttttgtaatgtaagaaatttatgacattaatatttagttttacatttgcagCGAGGTGTAAACTAGGGTATGAAGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC
cattaat putative branch site (score: 3)
taatgtaagaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattctcttttttttttaaagaaacataaaatttctaatattttgaccttttgtaatgtaagaaatttatgacattaatatttagttttacatttgcagCGAGGTGTAAACTAGGGTATGAAGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC
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