Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttttgatgcgtgtaagtaacgacgtcgttgcaatgcagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
Basic information
species | Oryza sativa |
transcript | LOC_Os09g28200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g28200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G088242_T01 (Zea mays), 3'ss of exon 1
---------gtaagcaaagcgccatgcc---gccaccttctgtagttctgttctctcgtgcgttt-tgatgcgtgtaagtaacgacgtcgttgcaa----------tgcagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
| ||| ||| || || | || || | || | || || | || ||| | | ||||| ||||||||||| |||||||||| |||||| |||||||||||| ||||||||||||| |||||||||||||||||||||| |||||||||||| |||||||||
gtgagtcgccttcgcacttggccttggtttagctaagccttggaggccgcgcggagcgcggacggatggtgaccgccggtgacggcaatgctgcaacgggcaataatgcagGGGTTCCGGAAGGTCGTCCCGGAGCGGTGGGAGTTCGGGAACGAGTTCTTCCGGAAGGGGGAGAAGCAGCTGCTGTGCGAGATCCACCGGCGGAAGACGT
upper sequence: LOC_Os09g28200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G04200.1 (Glycine max), 3'ss of exon 1
--------gtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttttgatgcgtgtaagtaacgacgtcgttgcaatg---cagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
| | | | | | | | || || ||| || | | | ||| | | | | || | ||| |||| || || ||| | ||||| || | ||||||||||||||||| ||||||| |||||| ||||| || |||| ||||||||| | || || |||
gtattatatttacttacacactgatacactatctctagttcttcaattattgttttcttttctttttatattc-tgacagttttaaatggatgaactagGGTTTTAGAAAGATTGTGCCAGACCGATGGGAGTTCGCGAACGAATTCTTCAAGAAGGGAGAGAAACACTTGCTGTGCGAGATCCATAGAAGAAAAACGG
upper sequence: LOC_Os09g28200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S19_153V6.1 (Physcomitrella patens), 3'ss of exon 1
----gtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttt--tgatgcgt----gtaagtaacgacgt-cgttgcaatg-cagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
| ||| | | || |||| | || || | | | | || | | | || | |||| ||| || ||||| ||||||||||| ||||| || ||||||||||||||||||| || ||| | || ||| ||| || || |||||| || | ||||| | |
taattttcgcaggtttcaggatcccctagctctggacttatggccgtgcacaaagctgataatcctttgctgaaactcttcacgtgcgtgatggtgacagGGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTCCGACGAGGAGAGCGGCACCTCCTTTGCGAGATATACAGGCGGAAGGCAT
upper sequence: LOC_Os09g28200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ38003 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------gtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttttgatg------cgtgtaagtaacgacgtcgttgcaatgcagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
| || | || || | | || | || | | || | || | | | | || | || ||||||| ||| | ||||| || || || | ||||| |||||||||||||||||| | ||||||||| ||||| || | ||||||||||| ||||||
gtgagttccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgttttgctttgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtg-tgcagGGATTCCGCAAGGTGGTTCCCGATCGCTGGGAATTCGCGAACGAGTTCTTCCGCAAGGGGGAGCGCCAGCTACTGTCGGAGATCCACCGGAGGAAG----
upper sequence: LOC_Os09g28200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ31857 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------gtaagcaaagcgccatgccgcca---ccttctgtagttctgttctct--cgtgcgttttgatgcgtgtaag--------taacgacgt-----cgttgcaa----------tgcagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
| ||| |||| | | |||| | ||||| | ||| | || ||| | || ||| | | || | |||||| ||||||| ||| | ||||| || || || | ||||| |||||||||||||||||| | ||||||||| ||||| || | ||||||||||| ||||||
gtgagttccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgtttgcttcgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcagGGATTCCGCAAGGTGGTTCCCGATCGCTGGGAATTCGCGAACGAGTTCTTCCGCAAGGGGGAGCGCCAGCTACTGTCGGAGATCCACCGGAGGAAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgttctctcgtgcgttttgatgcgtgtaagtaacgacgtcgttgcaatgcagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
aagtaac putative branch site (score: 2)
ttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttttgatgcgtgtaagtaacgacgtcgttgcaatgcagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA