Sequence
atgc intronic sequence ATGC exonic sequencegcaagtttctcttgattattcccaatatgatcatttcctttttctggccggtaactgtatggagctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46340.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
-gcaagtttctcttgattattcccaatatgatcatttcctttttctggccggtaactgtatggagctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
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aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttttgcc-------aacttttag----gtaag--atttgtaacttttccacctgctgttta-cagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 7
gcaagtttctcttgattattcccaatatgatcatttcctttttctggccggtaact-gtatgg-agctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
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-------------attcattagaaacttagaaactacattttttcagttttaattttgtctgttatttctaagtaatggttcatctgttcaagcttttgttccatttgtt--cagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 7
gcaagtttctcttgattattcccaatatgatcatttcctttttctggccggtaact-gtatgg-agctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
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-------------attcattagaaacttagaaactacattctttcagttttaattttgtctgttatttctaagtaatggttcatctgttcaagcttttgttccatctgtt--cagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 1
gcaagtttctcttgattattcccaa-tatgatcatttcctttttc-tggccggtaactgtatggagctcttactgccgctggctatatacagtc-tcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
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----gttttactttatttttattatctattattgcttgcaatgccattgttacatagtgcaatttgcctcaaataattttctgagcttggatttgtcttctttttctttttaacagGTTCTATTTCTAATGTACCACTACTTTGCTGCTGCGGAGATATACAATGCAATTCGTGTCTTTATTGCTGCATATGTCTGGATGACTGGATTTGGAAACTMapped 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|116424668|gb|EG467260.1|EG467260EST: TTCTTTACCTTAATCGCCACCAAACTGAAGAATGGAAAGGATGGATGCAG GTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCA
genomic: TTCTTTACCTTAATCGCCACCAAACTGAAGAATGGAAAGGATGGATGCAGgcaagtttct ... tttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggagctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
gacttac putative branch site (score: 2)
cttacttttt CT-rich tract
ttactttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtttctcttgattattcccaatatgatcatttcctttttctggccggtaactgtatggagctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT