Sequence
atgc intronic sequence ATGC exonic sequence...tgaattagattcaatagtcgtttttcgttttgctgaatcgatgttattctgaattttagttgaaatttcttaaaaactgtagctggtgtttcctctgcagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51690.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 1
tgaattagattcaatagtcgtttttcgttttgctgaatcgatgttattctgaattttag---ttgaaatttcttaaaaactgtagctggtgtttc-ctctgcagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA
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---actttgttgggaagt-gtggtttttttagtgtatgtattgttggatgaaatctgcgagattcctattttctttgcttctaatgtggtgtttcattttgcagTTGATATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAA
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 1
------tgaattagattcaatagt-cgtttttcgttttgctgaatcgatgttattctgaattttagttgaaatttcttaaaaac-tgtagctggtgtttcctctgcagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA
| | || | | | | ||||||| | | |||| ||| | | || ||||| || | | | | ||||| ||||||||| || ||||| || ||||| || ||||| ||||| | || | || ||||| ||| | |||||||||||||| ||||| |||||||||||| ||
ggaagggatagttaatccgccaacatggatctcgttttcat--actcgtgtt-cgatgatgtgaaattcaaattaattcatttcacattgttggtg-----aatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 1
tgaattagattcaata-gtcgtttttcgttttgctgaatcgatgttattctgaatt--ttagttgaaatttcttaaaaactgtagctggtgtttcctctg----cagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA
|| | | || |||| | || || || || | || | | ||| ||| || || | || || |||| | | || |||||||||| ||||| || ||||| |||||||| ||||| | ||| | || ||||| ||| | |||||||| ||||| ||||| |||||||| ||| |||
----ttgtctggagcgtgtaccttttagattagccttatttttgc-actcggtgtcaattatttggaacttaatttaatct--agctcgcactgttgatgaatgcagTTGATATTATCTCGGCTATTGAGTTTGATAAGACTGGAGAACATTTGGCGACTGGCGACAGAGGAGGACGCGTTGTACTTTTTGAGAGAACAGATGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctgaattttagttgaaatttcttaaaaactgtagctggtgtttcctctgcagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA
tgtttcctct CT-rich tract
aattttagttgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaattagattcaatagtcgtttttcgttttgctgaatcgatgttattctgaattttagttgaaatttcttaaaaactgtagctggtgtttcctctgcagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA