Sequence
atgc intronic sequence ATGC exonic sequence...tctctttgcttacgcacgtagaaaccgggttgtagaccgtagagcatgtcacgcgccggtgctaatgacgtgttaccttcgtgtgatcgatcggtcacagGTGGTCCATGATCGCCGCGCAGCTGCCTGGTCGGACGGACAACGAGATCAAGAATTACTGGAACACCAACGTCAAGAAGCAGCTCCGCCAGGGCCAGGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g45060.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g45060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G123202_T01 (Zea mays), 3'ss of exon 3
tctctttgcttacgcacgtagaaaccgggttgtagaccgtagagcatgtcacgcgccggtgctaatg--acgtgttaccttcgtgtgatcgatcggtcacagGTGGTCCATGATCGCCGCGCAGCTGCCTGGTCGGACGGACAACGAGATCAAGAATTACTGGAACACCAACGTCAAGAAGCAGCTCCGCCAGGGCCAGGCG---
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---------gtaaaagtctcgagcctaaactccgtactctctctctcctcacgcgccgtcaccgtcagtacgtgctggaacgttgtggt--gtcgatc--agGTGGTCCACGATCGCGGCACAGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATGAAGCAGCAGCTCCGACAGG---AGGCGCTC
upper sequence: LOC_Os04g45060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
tctctttgcttacgcacgtagaaaccgggttgtagac-cgta-gagcatgtcacgcgccggtgctaatgacgtgttaccttcgtgtgatcgatcggtcacagGTGGTCCATGATCGCCGCGCAGCTGCCTGGTCGGACGGACAACGAGATCAAGAATTACTGGAACACCAACGTCAAGAAGCAGCTC-CGCCAGGGCCAGGCG
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tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcgtggagcacagaaaa-attgattttttggaat-gtgttgttgttgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtcacgcgccggtgctaatgacgtgttaccttcgtgtgatcgatcggtcacagGTGGTCCATGATCGCCGCGCAGCTGCCTGGTCGGACGGACAACGAGATCAAGAATTACTGGAACACCAACGTCAAGAAGCAGCTCCGCCAGGGCCAGGCG
tgctaat putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctctttgcttacgcacgtagaaaccgggttgtagaccgtagagcatgtcacgcgccggtgctaatgacgtgttaccttcgtgtgatcgatcggtcacagGTGGTCCATGATCGCCGCGCAGCTGCCTGGTCGGACGGACAACGAGATCAAGAATTACTGGAACACCAACGTCAAGAAGCAGCTCCGCCAGGGCCAGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - tgcttac
- - - - - - - - - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gccggtg