Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttgacacagatctctaatcctacttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G20930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G08250.2 (Glycine max), 3'ss of exon 2
--------------gtaaaaatcgt---ctttgttttggaagaactatgacttgagataacccattttgacacagatctc----taatcctacttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
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gtagtacttaacccttaacccttgttccctttcatttccctcactcatg-tatgtaactatgtatgtatgtacatattatgaaataatttgaatttttatttatttatta-agGGACTTGAAGCCTCACAATCTGTTGATGGACCGGAAAACAATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGGGCATTTACTGTGCCAATTAAGAAA
upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G39760.1 (Glycine max), 3'ss of exon 2
gtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttgacacagatctctaatcctacttg---tcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
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---------------gtatgtagttaaccctaattccctttcatttctctcacaccatccttccgatttgaactggatctttaatctttatttagGGACTTGAAGCCTCACAATCTCTTGATGGACCGAAAAACCATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGAGCATTTACCGTGCCAATTAAGAAA
upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G07640.1 (Glycine max), 3'ss of exon 3
gtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttga-cacagatctctaatcctacttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
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---------gtactagtaatt-aacccttaacccttgttccctttcatttccctcacacgtgtataattgaatttttacttattt-atta-agGGACTTGAAACCTCACAATCTGTTGATGGACCGAAAAACAATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGGGCATTTACTGTGCCAATTAAGAAA
upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G38210.1 (Glycine max), 3'ss of exon 1
gtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttgacacagatctctaatcctacttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
| ||| | | | | | | | | || | | || | | || |||| || |||| ||||| | || |||||||||||||||||||||| || || |||| ||| ||||| || ||||||||| | || |||| || ||| | || || || ||
------ggtactctagttccctttcatttctctc-----acacctccttcgaatatcaattgatgaatctttcaatctttatt--atta-aGGGACTTGAAACCTCACAATCTCTTGATGGACCCAAAAACCATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGAGCATTTACTGTGCCGATTAAGAA-
upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttgacacagatctctaatcctac-ttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
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gtgacaattctctttctccctcga-atctccatctt---------ctttctcaaatgggtcctttctctgaaactgttttaaactcc---cagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAGMapped 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|19877265|gb|AU238096.1|AU238096EST: CAGTTATGCAAAGGCATGGCTTTTTGCCATGGTCATGGAGTGTTGCACAG GGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAA
genomic: CAGTTATGCAAAGGCATGGCTTTTTGCCATGGTCATGGAGTGTTGCACAGgtaaaaatcg ... ttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agataacccattttgacacagatctctaatcctacttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
ctctaat putative branch site (score: 3)
tttcatt putative PPT
tttcatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttgacacagatctctaatcctacttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT