Sequence
atgc intronic sequence ATGC exonic sequence...gcagggctcatttatgagtgaaaagagtgaggcgacgtcatttctcctactatttactggaacttccgccctactgatttgttttccttgggcatgacagTGCACCAGAGAAGATTTTGTGGAAAGAGTTAAAACTCAACAAGGTGAAGGTTGTAATGTACATGGCTTTTTAGATGTCAGCAAAGTTGCAGGGAACTTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g41120.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G161019_T02 (Zea mays), 3'ss of exon 6
gcagggctcatttatgagtgaaaagagtgaggcgacgtcatttctcctactatttactggaacttccgccctactgatttgttttccttgggcatgacagTGCACCAGAGAAGATTTTGTGGAAAGAGTTAAAACTCAACAAGGTGAAGGTTGTAATGTACATGGCTTTTTAGATGTCAGCAAAGTTGCAGGGAACTTAC-------------------------
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-------------------------------------------------------------------------tccactggtgtttgttgactgttttagtgtgcaagagaggattttattgatagagttaaaactcagcaagatgaaggttgcaatgtccttggctttttagATGTCAGTAAAGTTGCTGGAAATTTTCACTTCGCCCCAGGCAAAGGATTTTA
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G161019_T01 (Zea mays), 3'ss of exon 6
---gcagggctcatttatgagtgaaaagagtgaggcgacgtca-tttctcctactatttactggaacttccgccctactgatttgttttccttgggcatgacagTGCACCAGAGAAGATTTTGTGGAAAGAGTTAAAACTCAACAAGGTGAAGGTTGTAATGTACATGGCTTTTTAGATGTCAGCAAAGTTGCAGGGAACTTAC
| | | | | |||| |||| || ||| | | | | | |||| || || ||| | |||| | ||||| |||||| | || |||||||||||||| |||| ||||||||| ||||| | |||||||||||||||||| |||||||| || || || |
ggtttctaattagcatgtaactttttctggtgaacttttaaaggtttcctgcacactttttttattcctgagatccactg----gtgtttgttgactgttttagTGTGCAAGAGAGGATTTTATTGATAGAGTTAAAACTCAGCAAGATGAAGGTTGCAATGTCCTTGGCTTTTTAGATGTCAGTAAAGTTGCTGGAAATTTTC
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 6
gcagggctcatttatgagtgaaaagagtgaggcgacgtcatttctcctactatttactggaacttccgccctactga------tttgttttccttgggcatgacagTGCACCAGAGAAGATTTTGTGGAAAGAGTTAAAACTCAACAAGGTGAAGGTTGTAATGTACATGGCTTTTTAGATGTCAGCAAAGTTGCAGGGAACTTAC
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------gtttctaattagcaaacaactttttctggtgaactttttaaaagtttcctgcacactttctttattcctgagatccactggtgtttgttgactgttttagTGCGCAAGAGAGGATTTTGTTGAGAGAGTTAAAACTCAGCAAGATGAAGGCTGCAATGTCCATGGTTTTTTAGATGTCAGTAAAGTTGCTGGAAATTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctactatttactggaacttccgccctactgatttgttttccttgggcatgacagTGCACCAGAGAAGATTTTGTGGAAAGAGTTAAAACTCAACAAGGTGAAGGTTGTAATGTACATGGCTTTTTAGATGTCAGCAAAGTTGCAGGGAACTTAC
tactgat putative branch site (score: 2)
atttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcagggctcatttatgagtgaaaagagtgaggcgacgtcatttctcctactatttactggaacttccgccctactgatttgttttccttgggcatgacagTGCACCAGAGAAGATTTTGTGGAAAGAGTTAAAACTCAACAAGGTGAAGGTTGTAATGTACATGGCTTTTTAGATGTCAGCAAAGTTGCAGGGAACTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG