Sequence
atgc intronic sequence ATGC exonic sequence...tcattttaagctaggtttacttttttggagattctctgactggttggctgcattcatccattggttatttttaaaatgggtctctcaatcttcatgacagCTCTGCAGAAGCAGTTAATCGTATATATGAGATCAAAGGACGCGTACAGACACGGCCTCTTGCAATCTGTGTTGCTGATGTCCCAGACATATCACGGTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g10450.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g10450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G055217_T01 (Zea mays), 3'ss of exon 2
-----tcattttaagctaggtttacttttttggagattctctgactggttggctgcattcatcc--attggtt--atttttaaaatgggtctctcaatcttcatgacagCTCTGCAGAAGCAGTTAATCGTATATATGAGATCAAAGGACGCGTACAGACACGGCCTCTTGCAATCTGTGTTGCTGATGTCCCAGACATATCACGGTTT
|| || ||| | | | ||| || | |||| || || || | | || | ||||| | | |||||| || |||||||||||||||||||| ||||||||||||||| |||||||||||||||||| |||| ||| ||||||| ||||| ||||||| ||||||| |||||||||||||||||
acttatccattgaagatgagaatttcatttaggggtttctttgggtgtttcattttttgtattcttattggcttggtccttaaaa---------cactcttcatgacagCTCTGCAGGAGCAGTTAATCGTATTTATGAGATCAAAGGACGCATACAAACAAGGCCTCTGGCAATTTGTGTTGGTGATGTCTCAGACATATCACGGTTT
upper sequence: LOC_Os03g10450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g02920.t01 (Vitis vinifera), 3'ss of exon 2
tcattttaagctaggtttacttttttggagattctctgactggt--tggctgcattcatccattgg--ttatttttaaaatgggtctctcaat-----cttcatgacagCTCTGCAGAAGCAGTTAATCGTATATATGAGATCAAAGGACGCGTACAGACACGGCCTCTTGCAATCTGTGTTGCTGATGTCCCAGACATATCACGGTTT
||| | | | ||| || ||| | | | | | |||||| || || || | | || || | | | || ||| ||| |||||||||| ||| | ||||||||||||||||| ||| ||| ||| | ||||||||||| ||||||| ||||| |||||| || |||
------taatcataat---cctttatgaagaaacaacatccaatgatatttatattcatgagatgaaattgattatgcattgtttcctttcctgggggtgtaattgcagTTCTTCAGAAGCAGTCAATAGGATATATGAGATCAAAGGCCGCAAACATACAAGCCCTCTTGCAATTTGTGTTGGGGATGTATTGGACATACAGCGCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctgcattcatccattggttatttttaaaatgggtctctcaatcttcatgacagCTCTGCAGAAGCAGTTAATCGTATATATGAGATCAAAGGACGCGTACAGACACGGCCTCTTGCAATCTGTGTTGCTGATGTCCCAGACATATCACGGTTT
tcttcat CT-rich tract
attggttatttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcattttaagctaggtttacttttttggagattctctgactggttggctgcattcatccattggttatttttaaaatgggtctctcaatcttcatgacagCTCTGCAGAAGCAGTTAATCGTATATATGAGATCAAAGGACGCGTACAGACACGGCCTCTTGCAATCTGTGTTGCTGATGTCCCAGACATATCACGGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - tgactgg
- - - - - - - - - - - - - - - - - - - - - - - - tgcattc