Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgttacatttcatctatcatcgtggaagtcctttacatttttctattcgtagccaaatcatatcaataatgatatcagtatctggttattgttccagCGTGTGAAAGTATACCGTTTGACTGATGGAGGGAAATGGGATGATCGGGGCACAGGGCATGTAAATATTGACTTCCTTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23590.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23590.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G435675_T01 (Zea mays), 3'ss of exon 1
-gtgtgttacatttcatctatcatcgtggaagtcctttacatttttctattcgtagccaaat-catatcaataatgatatcagtatctggttattgttccagCGTGTGAAAGTATACCGTTTGACTGATGGAGGGAAATGGGATGATCGGGGCACAGGGCATGTAAATATTGACTTCCTTGAG
| || | | ||| | | || || || | | || | | | | || || | |||||| | | | | ||||||||||||| ||||||||||||||| ||||||| ||||| ||||| |||| || ||||| |||| |||||| | | |||||
ctttaattttaagaaacttatt-tgtcttatgttctgtatactatttatccctttactacatatgtactataaatgatggttacaattc-taactgttccagCGTGTCAAAGTATACCGTTTGGCTGATGGTGGGAAGTGGGACGATCAAGGAACAGGTTATGTTTCTATTGATTACATTGAG
upper sequence: LOC_Os01g23590.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S306_49V6.1 (Physcomitrella patens), 3'ss of exon 1
---gtgtgttacatttcatctatcatcgtggaagtcctttacatttttctattcgtagccaaatcatat-caataatgatatcagtatctggttattgttc-cagCGTGTGAAAGTATACCGTTTGACTGATGGAGGGAAATGGGATGATCGGGGCACAGGGCATGTAAATATTGACTTCCTTGAG
||| | |||| || |||| || ||| | || | |||| | ||| | | || | |||| || ||| || |||||| ||| | ||||| || ||||| |||| ||||| ||| |||||||||||| |||||||||| || || | | || | || |||
agaaggtgcaa-atttaatagttcat-gttacagtgatgataatgctg--attcctgaacaattgcgacgcatttttgatggtcgt-tcttgtacttgttcgcagAGAGTGAAGGTTTACCGATTGAATGATGAAGGTAAATGGGATGATAGGGGCACAGGTCACGTGTCTGTCGAATATCTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattcgtagccaaatcatatcaataatgatatcagtatctggttattgttccagCGTGTGAAAGTATACCGTTTGACTGATGGAGGGAAATGGGATGATCGGGGCACAGGGCATGTAAATATTGACTTCCTTGAG
ttgttcc CT-rich tract
aaatcatatcaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttacatttcatctatcatcgtggaagtcctttacatttttctattcgtagccaaatcatatcaataatgatatcagtatctggttattgttccagCGTGTGAAAGTATACCGTTTGACTGATGGAGGGAAATGGGATGATCGGGGCACAGGGCATGTAAATATTGACTTCCTTGAG
-tgtgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - -agccaaa