Sequence
atgc intronic sequence ATGC exonic sequenceAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaatatatttgcaattaaatcatgtgacttcattatcccactactaatctaagtacttgacttttatatatag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16180.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g54990.2 (Oryza sativa), 5'ss of exon 3
AGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaata----------tatttgcaattaaatcatgtgacttcatta-----tcccactactaatctaagtacttgact--tttatatatag------------
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AGTTTGGATCTGGACTGTTCCTGCTTGTTCAGGTTGTTCTTTTGTTGGACTTTGTTCATGGATGGAACGAGAATTGGGTTGCCAAGGATGAACAGTTCTGgttagtagctgatcttttccttgtttaccttcaggtccccttaatttagtatgaacttcttctgtttatcaaaacctgttaataatttgttcatatttattactgcag
upper sequence: AT1G16180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G46830.3 (Glycine max), 5'ss of exon 3
AGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaatatatttgcaattaaatcatgtgacttcattatcccactactaatctaagtacttgacttttatatatag---------------------------------------------
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AGTTTGGCTCGGGCATGTTTCTTCTTGTTCAAGTCATGCTCTTGTTGGATTTTGTTCATGGATGGAATGACAAATGGGTTGGATATGATGAACAATTCTGgttagttttaggctttgcttttctttt-tcttttttttctactgtaacgttatttcctttacttgataagttgacattatatttttgaatgagaatttcagtatttaccggtttatttatacag
upper sequence: AT1G16180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G36750.1 (Glycine max), 5'ss of exon 3
AGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaatatatttgcaattaaatcatgtgacttcattatcccactactaatctaagtacttgacttttatatatag----------------------------------
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AGTTTGGCTCAGGCATGTTTCTTCTTGTTCAAGTCATGCTCTTGTTGGATTTTGTTCATGGATGGAATGACAAATGGGTTGGATTTGACGAACAATTCTGgttagttttaggctttgcttttctattttacttctgtaacgtcatttcctttacttgataagttgacatatttttgaacgagaatttcagtatttacctgtttatttatacag
upper sequence: AT1G16180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0018g01420.t01 (Vitis vinifera), 5'ss of exon 4
AGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaatatatttgcaattaaat-catgtgacttcattatcccactactaatctaagtactt--gacttttatatatag----------------------------------------------------------------
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AGTTCGGCTCAGGACTGTTTCTTCTTGTTCAAGTTGTGCTTTTATTGGATTTTGTTCATAGATGGAATGACACATGGGTTGGATATGGAGAGCAATTTTGgttagt---tttggttattatcatattcttgctgtatctcttctttgtta-tcatctaaaaacctctgattgttttatctcgatttcatttttgtattttttttaatcaatttttatgcctgtattttactttttgaacattacagMapped 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|124859615|gb|EH944052.1|EH944052EST: TTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTG GTATGCTGCTTTG
genomic: TTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaat ... ttatatatagGTATGCTGCTTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGACGAGCAGTTCTGgttagtaaatatatttgcaattaaatcatgtgacttcattatcccactactaatctaagtacttgacttttatatatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG