Sequence
atgc intronic sequence ATGC exonic sequencegtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatctactcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g48290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g48290.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 4
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatctactcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
| ||| | ||||||| | ||| ||| | || | | | | || | ||||||||| | | |||| || ||| || |||| || ||||| || || | || ||||| || || ||||| || ||||| || ||||||||||||||||| ||||||| || ||||| || |||||||||||||
----------------gtaaaatc----tcttcttcactcatt-----actgtatgtggtggtgataaatgattttattttctactcataa-----ctaatt------catata-----tcttggatgtgataactgcagGATAAAATTTTGCAGTCAACAGGTAGAGGACGTGAAGTTACTGTCACTAATGATGGTGCTACAATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTA
upper sequence: LOC_Os05g48290.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 4
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgat-attggctcaaattttaatctactcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
| ||| | || | | ||| | | |||| | | || | | | ||| | | | || || | || ||||| || || | || ||||| || || ||||| || ||||| || |||||||| |||||||| ||||||| || ||||| || |||||||||||||
--------------------------------------------gtaaaatctcctcttcactcattatatgtggtggtaataaa-tgattttattttctactcataactaatttatatatcttggatttgataactgcagGATAAAATTTTGCAGTCAACAGGTAGAGGACGTGAAGTTACTGTCACGAATGATGGCGCTACAATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTA
upper sequence: LOC_Os05g48290.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatctactcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
| || | | | |||| | || | || || || || | ||| | || || ||||| ||| | | | |||| || ||| | ||||| ||||| || || | || |||||||| || ||||||||||| ||||| ||||| ||||| || |||||||| || ||||
--------------------------------------------gtaatttccgatctctgaatatttagaaagctacaaactttcaatttggttct--attgattattgttgaat--cctttttattat---tgtttagGATAAAATCTTGCAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTA
upper sequence: LOC_Os05g48290.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatct--actcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
|||| || | ||| | |||||| || || | | | | | | || | ||| || | | | || ||||||| || | || | ||| | | ||||| || || | |||||||| ||||| || |||||||| ||||||||||||||||||||||| || | ||||| |||||||| ||||||||||||||||
--------------gtaaacttctcttctcatctccctttattgctgaattagaagctgtt-tgtgtctttaagtattagccttggtttgtaatttgattaatttgtc------tatttg--ttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAMapped 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|58673994|gb|CK062680.1|CK062680EST: GTATGGCAATCAGTGATTTGGTCAAGACAACGTTGGGGCCAAAAGGAATG GACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAAT
genomic: GTATGGCAATCAGTGATTTGGTCAAGACAACGTTGGGGCCAAAAGGAATGgtatgctcaa ... ctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAAT
EST:
gi|3768427|gb|AU032454.1|AU032454EST: GTATGGCAATCAGTGATTTGGTCAAGACAACGTTGGGGCCAAAAGGAATG GACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAAT
genomic: GTATGGCAATCAGTGATTTGGTCAAGACAACGTTGGGGCCAAAAGGAATGgtatgctcaa ... ctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAAT
EST:
gi|88358247|gb|CI605172.1|CI605172EST: GTATGGCAATCAGTGATTTGGTCAAGACAACGTTGGGGCCAAAAGGAATG GACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAAT
genomic: GTATGGCAATCAGTGATTTGGTCAAGACAACGTTGGGGCCAAAAGGAATGgtatgctcaa ... ctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
acataac putative branch site (score: 3)
cctttctatgttct putative PPT
aaatttgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatctactcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT