Sequence
atgc intronic sequence ATGC exonic sequence...cttatgttgaccttttgattttatcctatttttacagtatcttttcagaagacagttctaatttcgtctttatattcttctcataatttgagaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------cttatgttgaccttttgat----tttatcctatttttacagtatcttttcagaagacagttctaatttcgtctttatattcttctcataat-ttgagaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
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gtttgtacctttcccctgtacattttttttcaaagttcaaacacaagccttgtggtattctttatttttgtcacttaatgtgttgtct-aacatggcttcatggtgcccctattgatgattcaatattgttcacatttccagGGCTGCTTATAAAGGATTTGCAGATTCTGTACGCCTCCTTTTGTTTTTGGGTGCATATAGGGGGCGGCAAGATAAAGAAG
upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G087806_T01 (Zea mays), 3'ss of exon 3
--------------cttatgttgaccttttgattttatcctatttttaca-gtat-cttttcagaagacagttct----aattt---cgtctt----tatattcttctca-taatttgagaaattc------agGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
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gtttgtacttgtgttatatgtttctcatttgcctccttgtaatttctgcttgtgcactttgtagaatactgccctgctgaatttaaacatcttgctgcttatttctctctctgtttttacatattctcttctagGGCTGCTTATAAGGGATTTGCAGACTCCATACGGCTTCTTTTGTTTTTGGATGCTTATAGGGGACGGCAAGACAAAGAAG
upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G024437_T01 (Zea mays), 3'ss of exon 3
-----------------------cttatgttgaccttt-tgattttatcctat---ttttacagtatcttttcagaagacagttctaatttcgtctttatattcttctc-ataatttgagaaattc-----agGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
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gtttgtgcttgtgttgtatatttctcatttgcctctttgtaatttctgcttgtgcactttgtaacatactgcccttctgaattttaacatttttctgcttatttctctctgttttttgcatatttctttctagGGCTGCTTATAAGGGATTTGCGGACTCCATACGGCTTCTTTTGTTTTTGGATGCTTATAGGGGACGGCAAGACAAAGAAG
upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 3
-cttatgttgaccttttgattttatcctatttttacagtatcttttcagaagacagttctaatttcgtctttatattcttctcataatttgagaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
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cttcaacttagaatttcgaatg-gttctgcttatgtgaaatatttacttaattcttcactttttaagtgctttaatagattcttcccttcttgaattttagGGCTGCATACAAAGGTTTTGCCGATTCTATACGTCTTCTGTTATTTCTTGATGCACACAGGGGACGTCAAGATACGGGGG
upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 3
cttatgttgaccttttgattttatcc-tatttttacagtatctttt--cagaagacagttctaatttcgtctttatattcttctcataatttgagaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
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-aaatccttatattttttttttgtgcatgaaaataggaaaactttcagcatgagatacttacagctgaaattctgtaatatttttct--ctggagaattgtagGGCTGCTTATAAAGGTTTTGCCGATTGTATACGTCTTCTTTTATTTCTGGACGCATATAGGGGACGCCAGGATAAAGAGGMapped 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|47829279|gb|CK118963.1|CK118963EST: AATGCTGATCCTGACGTGCCTGATAATGATGGAAGAAGCCCCTTGCATTG GGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGA
genomic: AATGCTGATCCTGACGTGCCTGATAATGATGGAAGAAGCCCCTTGCATTGgtatgcttgc ... agaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagaagacagttctaatttcgtctttatattcttctcataatttgagaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
ttctaat putative branch site (score: 2)
tttatattcttctcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttatgttgaccttttgattttatcctatttttacagtatcttttcagaagacagttctaatttcgtctttatattcttctcataatttgagaaattcagGGCTGCATATAAAGGTTTTGCAGATTCCATTCGCCTACTTTTATTTCTAGATGCATATAGAGGACGACAAGACAAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -gaagaca