Sequence
atgc intronic sequence ATGC exonic sequencegtatgctacttgacttttgctaagggggttttcttttctttgtttttgtactctttgctgcttgggatattgtaagaatccttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34910.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34910.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G29360.1 (Glycine max), 3'ss of exon 9
gtatgctacttgacttttgctaagggggttttcttttctttgtttttgtactctttgctgcttgggatattgtaagaatccttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
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---------------------aattggtaattttcatcttctggtttata-tccatgtttcatgggg-------agagtgcctgttcaccaaaaccagt-tagttaatgctttct-----cttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
upper sequence: AT4G34910.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G37930.1 (Glycine max), 3'ss of exon 3
-----------------------------------gtatgctac-ttgac-ttttgctaagggggt-tttcttttctttgtttttgtactctttgctgcttgggatatt---------gtaagaatccttcttttctttg------ctctatactcttaacct--tcccttaaacctttttt------atgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
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gtatgcaagtcctctcttatatctctgttatatttgtgtctaacattgacattttgctctgcatatgccatttttagtaagagttgcatactatgttaattggtaaattcatcttctggtttatatccatgtttcatggggagagtccctgttcagcgaaaccagttagttaatgctttctcttgttgatgaacagGTTATAAACTTTGAAATGCCTGAAAGTGTAGCGGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
upper sequence: AT4G34910.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0441g00010.t01 (Vitis vinifera), 3'ss of exon 8
gtatgctacttgacttttgctaagggggttttcttttctttgtttttgtactctttgctgcttgggatattgtaagaatccttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
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------------------------------gattttgcttgatgactgcaagttgtgaaatcagttacatgtgaaaatgacatctttggttagtattccatttaaaaacagatgtgttgcctttta-----acagGTTATAAATTTCGAAATGCCTCAAAATGCTCCAGGATATGTACATCGAATTGGACGTACTGGAAGAGCATATAATACTGGTGCATCTGTATCTCTT
upper sequence: AT4G34910.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0525g00010.t01 (Vitis vinifera), 3'ss of exon 2
gtatgctacttgacttttgctaagggggttttcttttctttgtttttgtactctttgctgcttgggatattgtaagaatccttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
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------------------------------gattttacttgatgactgccagttgtgaaatcagttacatgtgaaaatgacatccttggttagtattccatttaaaaacagatgtgttgcctttta-----acagGTTATAAATTTCGAAATGCCTCAAAATGCTCCAGGATATGTACATCGAATTGGACGTACTGGAAGAGCATATAATAGTGGTGCATCTGTATCTCTTMapped 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|164000345|gb|ES124758.1|ES124758EST: ATGCTGAGTTCGGTGTAGTTAGGGGAATTGATT-CAAAAAAGTTCACACG GTTATAAACTTTGATATGCCTCAAAGTGTTAC
genomic: ATGCTGAGTTCGGTGTAGTTAGGGGAATTGATTTCAAAAAAGTTCACACGgtatgctact ... ttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
tcttaac putative branch site (score: 2)
ccttttttat putative PPT
ttaaaccttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctacttgacttttgctaagggggttttcttttctttgtttttgtactctttgctgcttgggatattgtaagaatccttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA