Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcttgtaggtgcttctgtttctatttccggaacatccttactgagttactgactgattcgggggttgcagATATGAGGGTCAAATCTCAGCCAACAATATTGAAATTGGAGTTATTCGATCTGACCGTGAATTCAAGTATGTCATACAGACTTGATCAAGCTGTTTTTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g42320.4 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 10
gtatgtcttgtaggtgc-ttctgttt--ctatttccggaacatcct---tactgagttactgact---gattcgggggttgcagATATGAGGGTCAAATCTCAGCCAACAATATTGAAATTGGAGTTATTCGATCTGACCGTGAATTCAAGTATGTCATACAGACTTGATCAAGCTGTTTTTTA
|||| || | | || | || || || | || ||||| || | | | | || | ||| || ||||||||||||||| ||||| || ||||||| |||||||| ||| |||||||| |||| ||||| |||||
gtatcgctcgcatccctgttgtacttgcttagtttagaaatatcctaaatagttaataattggttccggatcttggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA----------------------------------
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G850355_T04 (Zea mays), 3'ss of exon 9
-----------------gtatgtcttgtaggt-gcttct-gtttctatttccggaacatccttactgagttactgactgattcgg-------gggttgcagATATGAGGGTCAAATCTCAGCCAACAATATTGAAATTGGAGTTATTCGATCTGACCGTGAATTCAAGTATGTCATACAGACTTGATCAAGCTGTTTTTTA
|| ||| | ||| | ||| || | |||||||| | | ||||||| | || ||| | | ||||||||||||||| ||||| || ||||||| |||||||| ||| |||||||| |||||||||| |||||
aattttgactttgaaagaagggtattgcaacccacttgtagttgcttagtttaaaacatcctaaat-agttactaattggttctgcatcttggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA----------------------------------
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G850355_T02 (Zea mays), 3'ss of exon 10
gtatgtcttgtaggt-gcttct-gtttctatttccggaacatccttactgagttactgactgattcgg-------gggttgcagATATGAGGGTCAAATCTCAGCCAACAATATTGAAATTGGAGTTATTCGATCTGACCGTGAATTCAAGTATGTCATACAGACTTGATCAAGCTGTTTTTTA
|| ||| | ||| | ||| || | |||||||| | | ||||||| | || ||| | | ||||||||||||||| ||||| || ||||||| |||||||| ||| |||||||| |||||||||| |||||
----gtattgcaacccacttgtagttgcttagtttaaaacatcctaaat-agttactaattggttctgcatcttggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA---------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttctatttccggaacatccttactgagttactgactgattcgggggttgcagATATGAGGGTCAAATCTCAGCCAACAATATTGAAATTGGAGTTATTCGATCTGACCGTGAATTCAAGTATGTCATACAGACTTGATCAAGCTGTTTTTTA
tattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcttgtaggtgcttctgtttctatttccggaacatccttactgagttactgactgattcgggggttgcagATATGAGGGTCAAATCTCAGCCAACAATATTGAAATTGGAGTTATTCGATCTGACCGTGAATTCAAGTATGTCATACAGACTTGATCAAGCTGTTTTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT