Sequence
atgc intronic sequence ATGC exonic sequence...gtattttatccatgctaaagcaactcttcatctactgtgctttaggacagtaaccacattcttaataattcgtaaattaagttcctagtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23610.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------------------------gtattttatccatgctaaagcaactcttcatctactgt-gcttta---ggacagtaaccacattcttaataattcgtaaattaagttcctagtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
| | ||| || | ||||| | | ||| | ||||| || || || | || |||| | | || ||| |||||| | ||| |||||||| || || || |||||||| |||||||||||||| ||||||||||| |||||||| || ||||| ||||| ||||| ||||| |||||||||||||
gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaac-caatctttacgactc-taatcattgttcctgct----tttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
gtattttatccatgctaaagcaactcttcatctactgtgctttaggacagtaaccacattcttaata-attcgtaaattaagttccta-------gtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
||| ||| || || | | | | | | | | | | || || || | || | || ||| | | || | ||| |||| ||||| | |||||| | || |||||||||||| | | |||||||| ||||| || |||||||| ||||| ||||| || ||||| ||||||||||
gtagttt---tatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------------gtattttatc-catgctaaagcaactcttcatctactgtg--ctttaggacagtaa----ccacattcttaataattcgt-------aaattaagttcctagtaaaattta-cagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
|| ||| | | | | | || | || ||| || ||| | || |||| || | ||| | || |||| ||| | || | | ||||||||||| |||| | || || || || || || | | ||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||| |
gtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcagCCACAAGCAAGAGCACTGGGAGAGAAAGAGGGTTTCAAAGTTAGTGTTGCCAAGACTAGCTTCAAAGCCAACACTAAGGCTCTCGCTGAGAATGAAGGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacagtaaccacattcttaataattcgtaaattaagttcctagtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
attcttaataattcgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttatccatgctaaagcaactcttcatctactgtgctttaggacagtaaccacattcttaataattcgtaaattaagttcctagtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG