Sequence
atgc intronic sequence ATGC exonic sequencegtcagtatcatccgcttgttcctttttattagtctatagtttagtagtttgctttctatggttgaagtctgagacaaaagttgttctgctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTATGAGCGAGGAAGAGATAAATGCACTTCCAGTTCACAAGTACAAGGTGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55530.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------gtcagtatcatccgc---ttgttcctttttattagtcta----tagtttagtagtttgctttctatggttgaagtctgagacaaaagttgttctgctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCAC---AACTTCTATGAGCGAGGAAGAGATAAATGCACTTCCAGTTCACAAGTACAAGGTGTT
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gttagtagttcttttcagtttttgtgatataaattcatactttgctacccatgataatttttagaactttttgaaaatgaattctgatagttaatttagctctagtctcttcagaagtgacatataat-atattcatatacagatttttctttccaatttcagATTATGAAACTTTAAGAGCTCTAGATTCAGATAATGTTTCTACTGCACCCTCCATGACCGAGGAAGAGATAAATGCTCTTCCTGTCCACAAATACAAGGT---
upper sequence: AT3G55530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 6
---------------------------------------gtcagtatc-atccgcttgttcctttttattagtctat---agtttagtagtttgctttctatggt--tgaagtctgagacaaaagttgttctgctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCA---CAACTTCTATGAGCGAGGAAGAGATAAATGCACTTCCAGTTCACAAGTACAAGGTGTT
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ggtttgtagttcttttcagtttttgatgtaaattcatactttgctacccatgaagaaaatgaattctgatagttaatttagctttagtctcttcagatgtgtcataatatattcatatacagatttttctttccaatttcaGATTATGAAACTTTAAGAGCTCTGGATTCTGATAATGTTTCTACTGCACCCTCTATGACGGAGGAAGAGATTAATGCTCTTCCTGTCCACAAATACAAGG----
upper sequence: AT3G55530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g05080.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------gtcagtatcatccgcttgttcctttttat-tagtctatagtttagtagtttgctttctatggttgaagtctgagacaaaagttgttc-tgctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTATGAGCGAGGAAGAGATAAATGCACTTCCAGTTCACAAGTACAAGGTGTT
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gtatggtcaagtcaattattgtgcaacatatgccatgcttcaaacttgaagttgaattcgtgcatttctttagaaattatcagaaggttctagctgaggtttattttgaaattgcacttatcatgaattattcattctgccacagATTATGAAACCTTGAGATCACTAGATTCTGATAATACTTCCTCAACTTCACTGAGTGAGGAAGAGATCAATGCTTTACCTGTTCACAAGTATAAGGTCACMapped 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|124777608|gb|EH867551.1|EH867551EST: ACTTAGGCTCCAGCTGGCTCTTCTTGATCGGGAATTTGATGACTTAG ATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACA
genomic: ACTTAGGCTCCAGCTGGCTCTTCTTGATCGGGAATTTGATGACTTAGgtcagtatca ... gctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACA
EST:
gi|86074728|gb|DR370485.1|DR370485EST: GAATTTGATGACTTAG ATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTA
genomic: GAATTTGATGACTTAGgtcagtatca ... gctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTA
EST:
gi|86078329|gb|DR374086.1|DR374086EST: CGGGAATTTGATGACTTAG ATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTA
genomic: CGGGAATTTGATGACTTAGgtcagtatca ... gctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtagtttgctttctatggttgaagtctgagacaaaagttgttctgctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTATGAGCGAGGAAGAGATAAATGCACTTCCAGTTCACAAGTACAAGGTGTT
ttctgct CT-rich tract
tttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtatcatccgcttgttcctttttattagtctatagtttagtagtttgctttctatggttgaagtctgagacaaaagttgttctgctgcaacagATTATGAAACTTTAAGAGCACTTGATTCTGATAATGTTTCCACAACTTCTATGAGCGAGGAAGAGATAAATGCACTTCCAGTTCACAAGTACAAGGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA