Sequence
atgc intronic sequence ATGC exonic sequence...gttaattctacataaagctgtcacagaaggaatggatgtctagttctcctcttgtacatatggttcttgatacttagtattttttcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12370.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 8
gttaattctacataaagctgtcacagaaggaatggatgtctagttct-cctcttgtacatatggttcttgatacttagt-attttttcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
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-ccttctttctgataatttgtgagtaaaggaatgca-gtatatctgtatgttttaaggattcatttttttcaacaaagttatttatgctacattaattgcagTTCAACCGCGGAACCAGTGCTATGCAACATTATGTTGCAACACGGCCAATGTTTATTGATGTGGATATTATGAGCATTGATATTCAAGTTGTTCTTGGTG
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 8
---------gttaattctacataaagctgtcacagaaggaat----ggatgtctagt-tctcctcttgtacatatggttcttgatacttagtattttttcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
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gtaataaagttttgttgtacataattacatttgagtgcacctactaacatatcaaatgttgaatttttggtaaattagtgcaactatttaactaaattactatttgtaatgcagTTTAACAGGGGTACAAGTGCCATGCAACATTATGTGGCAACACGTCCAATGTTTATTGATGTGGAAATAATGAATGCAGACACTAAGCTGGTTCTTGGTG
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 8
---------gttaattctacataa--agctgtcacagaaggaatgga--tgtctagttctcc-tcttgtacatatggttcttgatacttagtattttttcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
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gtaataaagttttgttgtacataattacatttgaatgcaccaactaacatatcaaatgctgaatttttggtaaataagtgcaactatttaacgaaattaatatttgcaatgcagTTTAACAGGGGTACAAGTGCCATGCAACATTATGTGGCTACTCGTCCAATGTTCATTGATGTGGAAATAATGAATGCAGACACTAAGCTGGTTCTTGGTG
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 8
gttaattctacataaagctgtcacagaaggaatggatgtctagttctcctcttgtacatatggttcttgatacttagtattttt-tcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
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-atggtgtagtttcaggttagatataataaatttgccaagaaattgtcaagctattgaaggatttctactctcttctaacccctatgtttttgctatgcagTTTAACAGGGGCACCAGTGCAATGCAGCATTATGTGGCAACACGTCCAATGTTTATTGATGTGGAGGTCATGAATGCAGATACCAGATTGGTTCTTGGTGMapped 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|164231501|gb|EL984073.1|EL984073EST: TTTTGTCACAG TTTAACAGGGGTACGAGTGCTATGCAACATTATGTGGCTACACGTCCAATG
genomic: TTTTGTCACAGgtgaatgctt ... tgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcctcttgtacatatggttcttgatacttagtattttttcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
tcttgat putative branch site (score: 4)
tattttttcttcttga CT-rich tract
atacttagtatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaattctacataaagctgtcacagaaggaatggatgtctagttctcctcttgtacatatggttcttgatacttagtattttttcttcttgattttcagTTTAACAGGGGTACAAGTGCTATGCAACATTATGTGGCTACACGTCCAATGTTTATTGATGTGGAAGTCATGAATTCAGACATTAGGTTGGTTCTTGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG