Sequence
atgc intronic sequence ATGC exonic sequencegtgagatctctttcttttgtttatgcttttgacaaagttttttttgtctgaattgatcaatgtttgggtcccctatgaaatatagctttgtgggtttgtcttttctgtttttgatagcttaatgtctctaaatcaatttgttatgctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGAACTGTCCTCATTCATAGTGCTGAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 4
gtgagatctctttcttttgtttatgcttttgacaaagttttttttgtctgaattgatcaatgtttgggtcccctatgaaatatagctttgtgggtttgtcttttctgtttttgatagcttaatgtctctaaatcaatttgttatgctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGAACTGTCCTCATTCATAGTGCTGAGCAG
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---------------------------------------------------aaaagcaagtgatccaatcct---tgacatcttggaacaaagtctaatattggctaatctttatactatcttgta-ctgagttcatttgtttgtgttgttttagGTTGCTGTGTTTGCTGGTGGTGTTGATACATCTGCAACTGAGACTAAAGGAACTGTCCTCATACATACAGCTGAGCAG
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 4
gtgagatctctttcttttgtttatgcttttgacaaagttttttttgtctgaattgatcaatgtttgggtcccctatgaaatatagctttgtgggtttgtcttttctgtttttgatagcttaatgtctctaaatcaatttgttatgctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGAACTGTCCTCATTCATAGTGCTGAGCAG
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-------------------------------------------ttctcgaaaagaagctattgttgatttct---tggaacaaagtctaata--------tttgcaaatctttatactatcttgta-ctgagttcttttgtttgtgttttttaagGTTGCTGTGTTTGCTAGTGGTGTTGATACATCTGCAACTGAGACTAAAGGAACTGTCCTCATACATACAGCTGAGCAG
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 4
gtgagatctctttcttttgtttatgcttttgacaaagttttttttgtctgaattgatcaatgtttgggtcccctatgaaatatagctttgtgggtttgtcttttctgtttttgatagcttaatgtctctaaatcaatttgttatgctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGAACTGTCCTCATTCATAGTGCTGAGCAG
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-----------------------------------------tttcacattcagtattaattttcttggttattttc---atatggcta-accatttagtgggagttcttgttgaccacttt---------aatca-tttattcacccttttgtagGTTGCTGTGTTTGCCAGTGGTGTTGATACCTCTGCAACAGAAACAAAAGGAACTGTCCTAATTCATAGTGCTGAGCAGMapped 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|124860627|gb|EH945064.1|EH945064EST: TGTTGGTAGCATTAAGCGAATGGAGAAAGCGAAG GTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGA
genomic: TGTTGGTAGCATTAAGCGAATGGAGAAAGCGAAGgtgagatctc ... ctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgtttttgatagcttaatgtctctaaatcaatttgttatgctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGAACTGTCCTCATTCATAGTGCTGAGCAG
ctctaaa putative branch site (score: 3)
tgctttcttc putative PPT
taaatcaatttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatctctttcttttgtttatgcttttgacaaagttttttttgtctgaattgatcaatgtttgggtcccctatgaaatatagctttgtgggtttgtcttttctgtttttgatagcttaatgtctctaaatcaatttgttatgctttcttcagGTTGCTGTATTTGCTGGTGGCGTTGATACCACTGCAACAGAGACCAAAGGAACTGTCCTCATTCATAGTGCTGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG