Sequence
atgc intronic sequence ATGC exonic sequence...ataagatcaaagtcccaaacgtcacttatttatgataacaaaatgatagtaatagtgatagatagtaattgtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
Basic information
species | Oryza sativa |
transcript | LOC_Os10g05690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
ataagatcaaagtcc-caaacgtcacttatttatgataacaaaatgatagta-atagtgatagatagtaattgtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
|| | | | || | || | || || || | || || | ||||| | | || | | | | | ||| || |||| ||| |||| |||| |||||||| || || | || ||||| |||||||| || ||||||||||| ||||||||||| || |||||||| ||||| ||
--gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
-------ataagatcaa--agtcccaaacgtcacttatttatgataacaaa--atgatagtaatag-----------tgatagatag--taatt------gtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
| | | || || | | ||||||| || | || |||| || |||| ||||| || | | ||| ||||| ||| | || |||| ||||| ||| ||||||||| || || | || || ||||||||||| ||||| |||||||| ||||||||||| || || || |||||||| ||
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------ataagatcaaagtcccaaacgtcacttatttatgataacaaaatgatagtaatagtgatagatag-taattgtaatagtgcatatattggga-ataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
| || | | ||| | | || || || | | | | |||||| | || | | ||||| | | | | ||| || || ||||| ||| ||| | || | ||||||||||| || |||||||| ||||||||||| || |||||||||| || ||
gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaacttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagtaatagtgatagatagtaattgtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
atagtaattgtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataagatcaaagtcccaaacgtcacttatttatgataacaaaatgatagtaatagtgatagatagtaattgtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
- - gatcaaa
- - - - - - - - - - - - - - - - - -taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcata