Sequence
atgc intronic sequence ATGC exonic sequenceatatcctttgctattaaatcttttgttttgcttcccgaaacaactttaactgtcaacagaagatattcgttagaccttaacatagttacacGTATGCTTATTTCAAGAAGCTGGACTACTTCTCCACTGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G76170.1 |
intron # | 6 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G76170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 6
-----atatcctttgctattaaatcttttgttttgcttcccgaaacaactttaactgtcaacagaagatattcgttagaccttaacatagttacacGTATGCTTATTTCAAGAAGCTGGACTACTTCTCCACTGAAT
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gttatatatcctt-attatgcaatatcccatatattctcatgtgatcttatgctctatttatcaattgtatgttattatccttgaccctatgacacgtatgcatatttcaaaaagCTGGACTACTTCTCCACAGAAT
upper sequence: AT1G76170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
atatcctttgctattaaatcttttgttttgcttcccgaaacaactttaactgtcaacagaagatattcgtta--gaccttaacatagttacacGTATGCTTATTTCAAGAAGCTGGACTACTTCTCCACTGAAT
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atatcctt-actatgcaatatcccatataatgtgatattatg-ctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
upper sequence: AT1G76170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G00350.3 (Glycine max), 3'ss of exon 1
----------------------atatcctttgctattaaat--------cttttgttttgcttcccgaaacaactttaactgtcaacagaagatat-----tcgttagaccttaacatagttacacGTATGCT-TATTTCAAGAAGCTG--GACTACTTCTCCACTGAAT-------------
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gtatgcttatttcaagaagctcgattacttttccaccgaatgtaaccttcctttcttttcctcttattttcccctctaactgccaaacaaacatttcactctctctacaattccagGCATTTACTCTCCTAATGCATATCGAGGTTTTGCTCGCGAGTTCATCAAAGATTTGGAGAGAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaacaactttaactgtcaacagaagatattcgttagaccttaacatagttacacGTATGCTTATTTCAAGAAGCTGGACTACTTCTCCACTGAAT
gaccttaac putative branch site
aactttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatcctttgctattaaatcttttgttttgcttcccgaaacaactttaactgtcaacagaagatattcgttagaccttaacatagttacacGTATGCTTATTTCAAGAAGCTGGACTACTTCTCCACTGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA