Sequence
atgc intronic sequence ATGC exonic sequencegttagtgaagttgtaccatttatttagcttcaaatgagggaccaggctttacattgataaattcaacatctttctctattgttgcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14210.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 13
---------gttagtgaagttgtaccatttatttagcttcaaatgagggaccaggctttacattgataaattcaacat----ctttctctattgttgcatgat--cagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
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gtgaggacattttgcaagagcgccccctatctgatatatcataggtaggtctaatagttggatgcacacttctctcacgttcctttcttttctgtctcactgttacagATCTGTTTACAAGACTATCCCGGACTGTGAACCTTGCCGACCTCTGCAAAGATCACCGATTGAAGGGTTCTATCTAGCTGGTGACTACACAAAGCAGAAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
gttagtgaagttgtaccatttatttagcttcaaatga--gggaccaggctttacattgataaattca-acatctttctctattgtt-------------gcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
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gtgaggatatttgctgaagacacttcctgacagataaccataagtagctctagctctgataattttatgtgttgttttctaatgtttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 12
------------------gttagtgaagttgtaccatttatttagcttcaaatgagggac-caggctttacattga--taaattcaacatctttct----ctattg-ttgcatgat--cagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
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gtttgattgaataaccagtctggcaatgtctttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAGATCTCCTTTAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
---------------------------------------------gttagtgaagttgtaccatttatttagcttcaaatgagggaccaggctttacattgataaattcaacatctttctctattgttgcatgat--cagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
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gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
-gttagtgaagttgtaccatttatttagcttcaaatgagggacca---ggctttacattgataaatt-caacatctttct-ctattgt-tgcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
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gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAAMapped 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|116473797|gb|EG516389.1|EG516389EST: GACCAAAGCAAAGCTAAAATTCTGAAGTACCATGTCGTTAAGACTCCAAG ATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAG
genomic: GACCAAAGCAAAGCTAAAATTCTGAAGTACCATGTCGTTAAGACTCCAAGgttagtgaag ... gcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaccaggctttacattgataaattcaacatctttctctattgttgcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
cattgat putative branch site (score: 4)
tttacattgataaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgaagttgtaccatttatttagcttcaaatgagggaccaggctttacattgataaattcaacatctttctctattgttgcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT