Sequence
atgc intronic sequence ATGC exonic sequencegtttaaaagaatccctcctgaaaccgaccatatcatgaatttcatatccaaatttgtttatcctggatttgattttgttgcttagGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCAACTATGCTTTCTCCTCTTGGAAAGGCCTGTGCAAAGATGGACCTTGCGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46570.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------gtttaaaagaatcc-------ctcctgaaaccgaccatatcatgaatttcatatccaaatttgtttatcctggatt--tgattttgttgcttagGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCAACTATGCTTTCTCCTCTTGGAAAGGCCTGTGCAAAGATGGACCTTGCGA
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gttttagtttttgttttagctttaaatgttgaacttcaatttacttttgctgtacttttattttcattccaaatgtattcaactttgtttttaaggtttaccttctcattctcgtaaaatcgctgttcacc-atgttgagttgcccccctttttttacagGTAACTTCTCATGTGTTAATGGGCTTAACTAAAAACACAGCAGTACTACCAACCATGCTTTCTCCTCTTGGAAAGGCTTGTGCAAGGATGGATCTCACTG
upper sequence: AT5G46570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------------------------gtttaaaagaatccctcctgaaaccgaccatatcatgaatttcatatccaaa-tttgtttatc---ctggatttgattttgttgctta--gGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACAC------AGTAATATTACCAACTATGCTTTCTCCTCTTGGAAAGGCCTGTGCAAAGATGGACCTTGCGA
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gtttggtttttgtttttgctttcaatgttgaccttcaatttacatttgctgttcttttatctccattccattccaactgtgttcaatttcattttcctggtttccttctctttgtctaaaatctttgttcatcattttgaatttgctccctctttttacagGTAGCATCTCTTGTGTTAATGGGCCTAACTAAAAACACCGCAGTGGCAGTGCTACCAACCATGCTTTCTCCTCTTGGAAAGGCTTGTGCTAGGATGGATC------
upper sequence: AT5G46570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0012g01140.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------gtttaaaagaatccctcctgaa-accgaccatatca---tgaatt-tcatatccaaatttgtttatcctggatttgat------------tttgttgcttagGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCAACTATGCTTTCTCCTCTTGGAAAGGCCTGTGCAAAGATGGACCTTGCGA
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gtgaaattttagtgaatctgtaacgttggaattacagttcatattagtttttgatgtacattaaatattctggtttgtgctgttatgtaatccttcatttgttcctaatatgctccagttattctctttggtattcagGTGGCATCTCATGTTCTAATGGGCCTGACTAAGACTACAGTTGTGCTGCCAACCATGCTGTCTCCTCTTGGAAAGGCTTGTGCAAGGATGGATCTTACTGMapped 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|47829701|gb|CK119385.1|CK119385EST: ATACCAAATTTCTTCTCTCTGCAGTAGCACCACTACAAAAGCAAGAAGAG GTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCA
genomic: ATACCAAATTTCTTCTCTCTGCAGTAGCACCACTACAAAAGCAAGAAGAGgtttaaaaga ... tgttgcttagGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatgaatttcatatccaaatttgtttatcctggatttgattttgttgcttagGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCAACTATGCTTTCTCCTCTTGGAAAGGCCTGTGCAAAGATGGACCTTGCGA
atttgat putative branch site (score: 5)
ttttgtt CT-rich tract
aaatttgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaaaagaatccctcctgaaaccgaccatatcatgaatttcatatccaaatttgtttatcctggatttgattttgttgcttagGTTGCTTCTCATGTCTTAATGGGCTTACCAAAGAACACAGTAATATTACCAACTATGCTTTCTCCTCTTGGAAAGGCCTGTGCAAAGATGGACCTTGCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA