Sequence
atgc intronic sequence ATGC exonic sequence...tagtatgtacaggacgctcatatcatggtgtggaccaatgttgacaacaatgtctccttgactagctcagcttagctcactcttcctcttccctttccagGTCGGTGATGCCAACAGGGACCACGCGTGCTGGGAGCGGCCGGAGGACATGGACACACCGAGGACCGTGTACAAGGTCGACCCGAGCACCCCGGGCACCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g21070.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g21070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G331566_T02 (Zea mays), 3'ss of exon 2
tagtatgtacaggacgc-tcatatcatggtgtggac--caatgttgacaacaatgtctccttgactagctcagcttagctcactcttcctcttccctttccagGTCGGTGATGCCAACAGGGACCACGCGTGCTGGGAGCGGCCGGAGGACATGGACACACCGAGGACCGTGTACAAGGTCGACCCGAGCACCCCGGGCACCG
|| | | || | | | || | | || || | | || | || || | || || | | |||| | | | | ||||||||||| || | || ||||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||| |||| |||||||||| |||
-agcaagcactgctggtgttgcgtctacacattggtggcagtgggggcg-caccgcaagctgatctgatcgatctccgcactcccttc-tgtggtcatcacagGTCGGTGACGCGACCAAGGACCACGCGTGCTGGGAGCGGCCGGAGGACATGGACACCCCCAGGACGGTGTACAAGGTGGACCGTGGCACCCCGGGATCCG
upper sequence: LOC_Os01g21070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G331566_T01 (Zea mays), 3'ss of exon 1
tagtatgtacaggacgctcatatcatggtgtggaccaatgttgacaacaatgtctccttgactagctcagcttagctcactcttcctcttccctttccagGTCGGTGATGCCAACAGGGACCACGCGTGCTGGGAGCGGCCGGAGGACATGGACACACCGAGGACCGTGTACAAGGTCGACCCGAGCACCCCGGGCACCG---------------------------------------------
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--------------------------------------------gcgcaccgcaagctgatctgatcgatctccgcactcccttc-tgtggtcatcacaggtcggtgacgcgaccaaggaccacgcgtgctgggagcggccggagGACATGGACACCCCCAGGACGGTGTACAAGGTGGACCGTGGCACCCCGGGATCCGACGTCGCCGCCGAGACTGCCGCGGCTCTCGCCGCCGCCTCCCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaatgtctccttgactagctcagcttagctcactcttcctcttccctttccagGTCGGTGATGCCAACAGGGACCACGCGTGCTGGGAGCGGCCGGAGGACATGGACACACCGAGGACCGTGTACAAGGTCGACCCGAGCACCCCGGGCACCG
agctcac putative branch site (score: 3)
cttagctcactcttcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtatgtacaggacgctcatatcatggtgtggaccaatgttgacaacaatgtctccttgactagctcagcttagctcactcttcctcttccctttccagGTCGGTGATGCCAACAGGGACCACGCGTGCTGGGAGCGGCCGGAGGACATGGACACACCGAGGACCGTGTACAAGGTCGACCCGAGCACCCCGGGCACCG
- - - - - - - - - - - -catggtg
- - - - - - - - - - - - - - - tggacca
- - - - - - - - - - - - - - - - - - -atgttga
- - - - - - - - - - - - - - - - - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttg