Sequence
atgc intronic sequence ATGC exonic sequencegtgactactatttcacctccctgtttcttagactactttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g24220.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 5
gtgactactatttcacc---tccctgtttcttagac--tactttatctcctcatgttatatacactaa-atgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
||| | | || |||| ||| | ||| | | | | | | || | | | | | | | | || | ||||||||||||| |||| || || ||||| ||||||||||| |||||||||||||| || || ||||||||||||||||| |||||||||||||| || ||||
gtgcattgtgttccaccacatcctcgcttcctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 10
gtg-actactatttcacctccctgtttcttagactactttatc---tcctcatgttatatacactaaatg--tcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
||| | | || ||||||| || ||| || | | || ||| | | | | || | ||| | || | ||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| || |||||||||||||| || || |||||||| ||||| |
gtgcatcggtgttccacctccttgcttcctata-tgtttcatcaagtatttaaagtcaatcctaatgatggcttcttcactcagGTTCCCTTTGCTCGCTCGTCGTTGAACCATGACGATGTCTTTATCTTGGACACTGAAAATAAGATATATCAATTCAACGGCGCCAACTCCAACATTCAGG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 4
-----gtgactactatttcacctccctgtttcttagactac---tttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
||| ||||| || | | | | | | | | || || || | | | | || || | | | ||| |||||||| ||||| || || ||| ||||||||||||||||||| ||| | || || | || || || ||||||||||||||||||||||||||||| || |
gcatagtgttctctatt-catgtacttttcaaatgcagtgcacattcattgactaaaaatgtg-atacaaagttttccttatgcagGTTCCTTTTGCACGGTCTTCACTGAATCATGATGATGTATTCATCCTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAACTCCAATATCCAGG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G32100.1 (Glycine max), 3'ss of exon 3
gtgactactatttcacctccctgtttcttagactactttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
| || | || ||| | ||| | || | | | || | | | || | | |||| || ||||| | || |||||||| ||||| |||||||| || | || || | || || || |||||||||||||||||||| ||||||||||| |
--gtatagtgtt----ctctattattcatgaacgtcataaattcagtgcgcatgaagtttgacattttggtttgatagGTCCCTTTTGCAAGGTCTTCATTGAACCATGAAGATGTATTCATACTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAATTCCAATATTCAGG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 5
-----------------------gtgactactatttcacctccctgtttcttagactactttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
| ||| | | || | | ||| | | || | ||| | | | | || || | | ||| ||||| || ||||| || || ||||||||||||||||||||||| ||| | || || | || || || ||||||||||||||||||||||||||||| || |
gtcagaataaaacaggcacaatgttctctattcatgtacttttcaaattcagtgcaca-ttcgttgcctaaaaatgtg-atacaaagttttgcttatgcagGTCCCTTTTGCACGGTCTTCATTGAATCATGATGATGTATTCATCCTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAACTCCAATATCCAGG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 4
gtgactactatttcacctccctgtttcttagactactttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
|| | | ||| | ||| | ||| | ||| || | | | | || | | ||||| || ||||| | || || ||||| ||||| |||||||| || | ||||| || || || || |||||||||||||||||||| ||||||||||| |
----gtatagtctt--ctctgttattcatgaacttcattaattcagtacgcatgaagtttgacattttgctttgacagGTCCCTTTTGCAAGGTCTTCGTTGAACCATGAAGATGTATTCATACTAGATACTGAGAACAAGATTTATCAATTCAATGGTGCAAATTCCAATATTCAGG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgactactatttcacctccctgtt--tcttagactactttatc-----tcctcatgttatatacactaaatgtcctatattc--agGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
|| | | || | | | ||| ||| || | | | | | |||| ||| | | || ||||||| ||||| ||||| || |||||||||||||||| ||||||||||| || | | || || ||||| || ||||||||||| || ||||| ||||
gttttctttgctgcagatttttagaagtgttacactctcttcgcatgagtgtttaatatgtatatacttatctcttttcttttgtagGTTCCTTTTGCACGCTCATCTCTGAATCATGATGATGTGTTTATCTTGGACACCAAGGAAAAGATTTATCAGTTTAATGGTGCAAATTCAAATATCCAAG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgactactatttcacctccctgtttcttagactact---------ttatctcctcatgtta----tatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
|| || ||| || ||| | | || | | ||| | | | | | | || || | | | |||||||| ||||| ||||| ||| |||||||||||||||||||||||||||| || || | || || ||||| |||||||||||||| || || ||||| |
gttttaaccattgtactctccttgtattagaacgagtgaacggtgattaccaatgtacatcaactttttcttctgttcctcttttttgcagGTTCCTTTTGCCCGCTCATCACTGAATCATGATGATGTATTTATCTTGGACACCGAGGAAAAGATCTATCAGTTCAATGGTGCAAATTCAAACATTCAGG
upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 4
gtgac-tactatttcacctccctgtttcttagactactttatctcctcatgttatataca-----ctaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
|| || | | || | | |||| | ||| | || || | | || || | | | ||||| || |||||||| || ||| | ||||| |||||||| |||||| |||| || ||||| ||||| ||||| |||||||||||||| |||||||| || |
gtagtatattctcccaacatg-tatttcatgatctaatcacgttcactgtgctgcagctggtcacctgcattttggttgtgcagGTCCCCTTTGCTCGGTCTTCACTAAATCACGATGATGTGTTTATCCTGGACACAGAAAATAAAATTTATCAGTTCAATGGTGCAAATTCCAATATCCAGGMapped 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|88725513|gb|CI748772.1|CI748772EST: AAACAAGGCTATATATTTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAG GTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTCGGAT
genomic: AAACAAGGCTATATATTTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgactacta ... ctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGAT
EST:
gi|11442605|gb|BF430508.1|BF430508EST: AAACAAGGCTATATATTTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAG GTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGAT
genomic: AAACAAGGCTATATATTTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgactacta ... ctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttagactactttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
cactaaa putative branch site (score: 2)
ttatatacactaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgactactatttcacctccctgtttcttagactactttatctcctcatgttatatacactaaatgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA