Sequence
atgc intronic sequence ATGC exonic sequence...tctgaaattttagatattctagttttcccagtaggcataaagaataaactaagtggtgcttcttttgattatgtgtttttgcatcctgtgtcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGGCTGGGCGAGTTTCATGGAAGCACCATACTTGCGTGCTTTCTGCCCTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g18010.3 (Oryza sativa), 3'ss of exon 3
tctgaaattttagat-attctagttttcccagtaggcataaagaataaactaagtggtgcttcttttgattatgtgtttttgcatcctgtgtcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGGCTGGGCGAGTTTCATGGAAGCACCATACTTGCGTGCTTTCTGCCCTTAG
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tctccttttgcattccatttatatattcatcactagtgctacaactatccaaatgtgaaaccttgctattcatgctgttttccatt-tatgatttctttagGTTATATTGAGCCTGTGTTGGTCATACTTCATGAGCAAGAGCCTACATGGGCTGGGCGTATCTTATCAAAGCACCATACATGCATGATATCTGCATTTAG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 4
--------------------------tctgaaattttagat-attctagttttcccagtaggcataaagaataaactaagtggtgcttcttttgattatgtgtttttgcatcctgtgtcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGGCTGGGCGAGTTTCATGGAAGCACCATACTTGCGTGCTTTCTGCCCTTAG
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gtgctggatctgcatatcatgaggagtctccttttgcattccatttatatattcatcactagtgctacaactatccaaatgtgaaaccttgctattcatgctgttttccatt-tatgatttctttagGTTATATTGAGCCTGTGTTGGTCATACTTCATGAGCAAGAGCCTACATGGGCTGGGCGTATCTTATCAAAGCACCATACATGCATGATATCTGCATTTAG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 4
tctgaaattttagatattctagttttcccagtaggcataaagaataaactaagtggtgcttcttttgattatgtgtttttgcatcctgtgtcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGGCTGGGCGAGTTTCATGGAAGCACCATACTTGCGTGCTTTCTGCCCTTAG
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--gtgagtacaaattaatgcaaatttgttgct--gcctttgaaccactccatatgatgatgatc---aatgcctgaatttg-ataatctgttttgt--agGTTATATTGAGCCTGTGATGGTAATTCTTCATGAGAGGGAGCTTACTTGGGCTGGGCGTGTCTCATGGAAGCATCATACTTGCATGATTTCTGCGCTTAGMapped 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|116380073|gb|EG422665.1|EG422665EST: CTTGCGTGATCTGGAAATGAAACACGTCAAAGATTTTGTTTTTCTACATG GTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGG
genomic: CTTGCGTGATCTGGAAATGAAACACGTCAAAGATTTTGTTTTTCTACATGgtaggtttag ... tcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactaagtggtgcttcttttgattatgtgtttttgcatcctgtgtcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGGCTGGGCGAGTTTCATGGAAGCACCATACTTGCGTGCTTTCTGCCCTTAG
ttttgat putative branch site (score: 4)
tcctgtgtcttcttc putative PPT
ttttgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgaaattttagatattctagttttcccagtaggcataaagaataaactaagtggtgcttcttttgattatgtgtttttgcatcctgtgtcttcttcagGTTATATTGAGCCTGTAATTGTCATCCTTCAGGAAGAAGAGCATACTTGGGCTGGGCGAGTTTCATGGAAGCACCATACTTGCGTGCTTTCTGCCCTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-ctgaaat
- - - - - - - - - - - - - - - - - -cataaag
- - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttttg