Sequence
atgc intronic sequence ATGC exonic sequence...gttgaataataatattttgctcttttggtcgaataatactttactcttttggttgaataatactttgctttgtctttgaattgtgaactcctatttacagGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62820.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G002276_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------gttgaataataatattttgctcttttggtcgaata---atactttactcttttggttgaata--atactttgctttgtctttgaattgtgaactcctatttacagGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG
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gtgtagctcttttcttttctgtgcaactcaactttgctgtccctggtataattcatgttacttggtcatactcaagtaactcaactct-ccattttgattggaaacaggtttcttatttttatagttgaatataatactttggtctgttcttaaacaat--agtcttatt-acagGTAGACCCCCTAGGCAAGGTTGACCCTGAAGTGGAGGATTTACTTCTAGAAATCGCCGATGACTTCATTGACTCG
upper sequence: LOC_Os01g62820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149230_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------gttgaataataatattttgctcttttggtcgaata---atactttactcttttggttgaata--atactttgctttgtctttgaattgtgaactcctatttacagGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG
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gtgatgacctggctctttttcttttctgtgctcctcaacttcactgtcactgatgtaattcatgttactggtcataatcagctctccattttgattggaaacaggtttcttatttttatagttgaatatagtactttgaactgttcttaaacaat--agttttatt-acagGTAGATCCCTTAGGCAAGGTTGACCCAGAAGTGGAGGATTTACTTCTAGAAATCGCTGATGACTTCATTGGCTCG
upper sequence: LOC_Os01g62820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g01420.t01 (Vitis vinifera), 3'ss of exon 3
-----gttgaataataatattttgctcttttggtcgaataatactttactcttttggttgaataatactttgctttgtctttgaattgtgaactcctatttacagGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG
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tgctcgttctgtt-tattatttttgatttttgattatttatta-ttcattttcacccaaaaataatagtttgtaat-tctgatcatctttgactcatgct--cagGTGGATTCACAAGGAAAGCTGGACCCTGAAGTTGAAGATCTTCTTTTGGAGATTGCTGATGACTTCATTGATTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttggttgaataatactttgctttgtctttgaattgtgaactcctatttacagGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG
ctcctattt CT-rich tract
ttgaataatacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaataataatattttgctcttttggtcgaataatactttactcttttggttgaataatactttgctttgtctttgaattgtgaactcctatttacagGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT