Sequence
atgc intronic sequence ATGC exonic sequencegtatgactccattcaccaacttgcttctcctttttgttctatttgatttaccttaaaactccagttctgcaaagtcttggagatgcttcaagttactgatttgaatataggtttctctaggagATCCTTTTTGATGAGTTTGTTATTGCCCATATCCTTGGATGGTGGGGGAAGGCTATAATGATAAGAAACCAACCACTTTTATGGGTATTATCAATTGGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g02890.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 6
---gtatgactccattcaccaacttgcttctcctttttgttctatttgatttaccttaaaactccagttctgcaa-----agtcttggagatgcttcaagttactgatttgaatataggtttctctaggagATCCTTTTTGATGAGTTTGTTATTGCCCATATCCTTGGATGGTGGGGGAAGGCTATAATGATAAGAAACCAACCACTTTTATGGGTATTATCAATTGGCT
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gtatgatgacttcattcaccaacttactt-tcctttttgttcaatttcgtttctcatatacttctgactaagcagtcttgactattcaatacgcttcaagttactgatttgaatatagttttttctagGAGATCATTTTTGATGAATTTGTTATAGCTCATATCCTTGGATGGTGGGGTAAGGCTATAATGATACGAAACCAACCACTTTTGTGGGTCTTGTCAATTG---
upper sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 6
---gtatgactccattcaccaacttgcttctcctttttgttctatttgatttaccttaaaactccagttctgca-----aagtcttggagatgcttcaagttactgatttgaatataggtttctctaggagATCCTTTTTGATGAGTTTGTTATTGCCCATATCCTTGGATGGTGGGGGAAGGCTATAATGATAAGAAACCAACCACTTTTATGGGTATTATCAATTGGCT
|||||| |||||||| || | ||| |||||||||||| |||| ||| | || | | | ||| | | || |||||||||||||||||||||||||||| ||| |||||||||| ||||||||||||||||||| || |||||||| ||||||||||| ||||||||||||||| |||||||||||||||| ||||| ||||||||||
gtatgatgacttcattcaccgacctactt-tcctttttgttcaatttcgtttctcatatacttttgactaagcactcttgactattcattatgcttcaagttactgatttgaatatagttttttctagGAGATAATTTTTGATGAGTTTGTTATCGCTCATATCCTCGGATGGTGGGGTAAGGCTATAATGATACGAAACCAACCACTTTTGTGGGTGTTATCAATTG---
upper sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 7
gtatgactccattca-ccaacttgcttctcctttttgttctatttgatttacc-ttaaaactccagttctgcaaagtcttggagatgcttcaagttactgatttgaatataggtttctctaggagATCCTTTTTGATGAGTTTGTTATTGCCCATATCCTTGGATGGTGGGGGAAGGCTATAATGATAAGAAACCAACCACTTTTATGGGTATTATCAATTGGCT
|||||| | | || | | | |||| || | || | | || | || || | || | | |||| || || | | ||||||| | | | | ||||||| | |||||||||||| |||||| | || ||||| ||||||||||||| |||||||||||||| | || || || || ||||||| | |||||||
gtatgatttctcacaatccattcacttcaaaattgt-ttgtgtatgttccactgttcctgacatacatcaatatgatattgg-gaggc--aagacttctgattt--tttctgttgtttctagGAAACCCTTTTTGATGAATTTGTTGTGGCTCATATATTTGGATGGTGGGGTAAGGCTATAATGATTCGCAATCAGCCCCTCCTATGGGTGCTGTCAATTG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaagtcttggagatgcttcaagttactgatttgaatataggtttctctaggagATCCTTTTTGATGAGTTTGTTATTGCCCATATCCTTGGATGGTGGGGGAAGGCTATAATGATAAGAAACCAACCACTTTTATGGGTATTATCAATTGGCT
tactgat putative branch site (score: 2)
tttctct putative PPT
atttgaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgactccattcaccaacttgcttctcctttttgttctatttgatttaccttaaaactccagttctgcaaagtcttggagatgcttcaagttactgatttgaatataggtttctctaggagATCCTTTTTGATGAGTTTGTTATTGCCCATATCCTTGGATGGTGGGGGAAGGCTATAATGATAAGAAACCAACCACTTTTATGGGTATTATCAATTGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA