Sequence
atgc intronic sequence ATGC exonic sequence...cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttgttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G38895.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 3'ss of exon 3
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagt--tctttgttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
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-gttgattgaaaaaaaaaactgacatcaaatctgttgttagcaccatgaaca-atttatctgcctaagattttgtactaattcttacattatatctatgcagATTATACTTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGT
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G468260_T02 (Zea mays), 3'ss of exon 2
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttgtt----ttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
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----gaacgaaaggtgttcaaaactatgagcattacattttttctgttgatactttataatcacattctcactattgttatatattaatgtaactaaattgcagATTATGATTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGT
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttg-ttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
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-attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggt--aatattggtttcatagttctttg-ttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
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--tgctgctattaact-tgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G50950.1 (Glycine max), 3'ss of exon 3
cattaggccattaatagtatagtttacgtagatgaggc-aatcgttgcgagtgcatta-aggtaatattggtttcatagttcttt--gttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT-
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---ggggtcgcc--tgctccgctccgtgatgacgggattgacaactatggaagcaatataacctccacaattcttacatttgtttcaattgtttttgcttgcagaATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTTGTTGTATTTATGAGTGGATGGAAAGAAGTGACAACTGTCCCGTT
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttgttttaacaatat------gcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
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----ttcccagaatttgaacttgtgacctccatgactctgt-gtcacaag-gcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
upper sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0083g01000.t01 (Vitis vinifera), 3'ss of exon 3
cattaggccattaatagt---atagtttacgtagatg-aggcaatcgttgcgagtgcattaaggta---atattggtttcatagttctttgttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
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-atcttgtcattattaggttgatgattctgttaactgtactcaaatatta-gaatgttttagggtatagattctgatttgttcatacttatcttt-----tatgcagAATATACTCCAGAAAATCCCAAGATAATGACAAAATGCTCTCACCATTTTCACCTTGGTTGTATATATGAATGGATGGAGAGAAGTGAAACATGTCCAGTMapped 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|164170907|gb|ES106763.1|ES106763EST: TTCGGATGATGAAGATATTTGTCCAACCTGCCTTGATG ATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCC
genomic: TTCGGATGATGAAGATATTTGTCCAACCTGCCTTGATGgtaatactaa ... caatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgagtgcattaaggtaatattggtttcatagttctttgttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
ttttaac putative branch site (score: 2)
tttgttttaacaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttgttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT