Sequence
atgc intronic sequence ATGC exonic sequence...ggaagttctttccccttggggccaaggtttttttttaatgcacaagatattttatctttgttggtctttgactgagtgttattaatttatttctgtgaagTCATCCCTGCTGAAAATGGCCAGCAAGCATGGACATATCTAGAAGATATGCAAAACAGCATTGATCTTGTTTTGACAGAGGTTGTTATGCCTGGTGTATC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g49460.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G033962_T01 (Zea mays), 3'ss of exon 1
-------------ggaagttcttt---ccccttggggccaaggtttttttttaatgcacaagatattttatct---ttgttggtctttgactgagtgtt--atta----atttatttctgtgaagTCATCCCTGCTGAAAATGGCCAGCAAGCATGGACATATCTAGAAGATATGCAAAACAGCATTGATCTTGTTTTGACAGAGGTTGTTATGCCTGGTGTATC
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gtcaacctccctgtgcagctccatgggccacgcgggtcccatagatatatataaataattttctattttctttgaccgactggtgttcttttaaaagtttagttgtgctatccaacctttttcagTTATCTCTGCCAAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGGGAAACAACATAGATCTTGTTTTGACTGAGGTTTTTATGCCCGGTGTATC
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 1
ggaagttctttccccttggggccaaggtttttttttaatgcacaagatat--tttatctttgttggtctttgactgagt--gttat-taatttatttctgtgaagTCATCCCTGCTGAAAATGGCCAGCAAGCATGGACATATCTAGAAGATATGCAAAACAGCATTGATCTTGTTTTGACAGAGGTTGTTATGCCTGGTGTATC
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-----gctgtgccaaacagggccaaaagactttgttgttgttgtttctttgactgattgttattgttctttaagaaatttagttatgctatccaacctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGAGAAACAACATAGATCTTGTTTTGACTGAGGTTTTTATGCCCGGTGTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatattttatctttgttggtctttgactgagtgttattaatttatttctgtgaagTCATCCCTGCTGAAAATGGCCAGCAAGCATGGACATATCTAGAAGATATGCAAAACAGCATTGATCTTGTTTTGACAGAGGTTGTTATGCCTGGTGTATC
tattaat putative branch site (score: 2)
tttatttct CT-rich tract
ttattaatttatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaagttctttccccttggggccaaggtttttttttaatgcacaagatattttatctttgttggtctttgactgagtgttattaatttatttctgtgaagTCATCCCTGCTGAAAATGGCCAGCAAGCATGGACATATCTAGAAGATATGCAAAACAGCATTGATCTTGTTTTGACAGAGGTTGTTATGCCTGGTGTATC
- - - - - - - - - - - - - - - - - - aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg