Sequence
atgc intronic sequence ATGC exonic sequence...ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g10600.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 4
-ttatagag-tatttttggagtaatatcctacgttttagtctgctttcagt-cttcagtga-tcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG
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ttcacttagctgccatgggaatatgttatcactttttgaggttcaaccaaaactccagcaagtcttaatagttttcatttcctctccc----attgttgcttagGTATCGGGCTCCCATCTAGGAAGTCACTTTTCCAACTACAAGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATG
upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtct---tcagtgatcttaagattcatggtgttcttttcctctgatttctgctc-agGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
| || | || ||| || | | ||||| | |||||| || | ||| | | || | ||| | || | || | | || || || |||||||||||||| |||||||| |||||||||||||| | |||||||| ||||| || |||||||| | || |||
-tctaagtaagttgtgg---tatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 5
--ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttca--gtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
| |||| || | ||| | | | | ||||| | |||||| || | | ||| | | || ||| | || || | | | ||| | || || || |||||||||||||| |||||||| |||||||||||||| | |||||||| ||||| || |||||||| | || |||
tatgtctaagtaagtt-gtggtatttttgt-cattttaatgtgctttgagggtaaatcatgaaatatatctttatg-tattattatattat-attatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttt---tcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
| || || |||| | ||| | | | | | |||||| | | || || | | |||| | || ||| | | | ||||| |||| || || |||||||| ||||||||||| || |||||||||||||||||||||||||| | || | || |||||||| || || |||
attcagtccatgtttgttg-aatttatagaggtggtttttattttcag--ataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 4
-ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttttcctctg--atttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
|| || |||| | ||| | | | | | |||||| | | || || | | |||| | || ||| | | ||||| |||| || || |||||||| ||||||||||| || |||||||||||||||||||||||||| | || | || |||||||| || || |||
nnntcagtccatgtttgttg-aatttatagaggtggtttttattttcag--ataattgttcctcaaattcttctgtttatttgtgtacgctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|218500747|gb|FG962718.1|FG962718EST: GCAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
genomic: GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCAgtaagttgtc ... ttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
EST:
gi|27576482|gb|CA999176.1|CA999176EST: AAGGGATGCTTCA GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
genomic: AAGGGATGCTTCAgtaagttgtc ... ttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
EST:
gi|29616664|gb|CB621676.1|CB621676EST: GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
genomic: GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCAgtaagttgtc ... ttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtcttcagtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG
ctctgat putative branch site (score: 4)
ttcttttcctctgatt CT-rich tract
ttaagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttttcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT