Sequence
atgc intronic sequence ATGC exonic sequencegtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11140.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatat-attttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
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gtgaactttgtt-acaacctccaaattttcttaattactgatccc-----------cccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
|| | || || | | | || |||| || | || || | | | |||| | | ||| | | || ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || || |||||| |||| |
gttattattccttcaaat---agtcattttagtactaatggtaaatgaaaatatgattctta-tgattttttt-------tgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
|| | |||||| | | | || |||| || | || || | | |||| | |||| |||| ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || ||||||||| | || |
gttattattgtttcaaat---agtcattttagtactaattgtaaatgaaaatatgactcttatgaaactttttgtta--------cagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
|| || | ||| | ||| | | | | | | | | | | || | | | | || ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||| ||| ||||||| ||||| ||||| ||||| || ||||||||| |||| |
------gttattattgtctcaaatagtcatttgagtactaatggtaag----tcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattt--tagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT------
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-----------------------------gttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattt--tagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
||| | | || || ||| | | || | ||||| || |||| | | || ||| | ||||| ||||||||||| ||||||||||||||||||||||| || ||||| || || |||||| || | |||||||||||||| |||||||| || || ||| | ||||
---------gttggggacactaaagttatttgttttattt-cctggcaacttt----ccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
----------------------gtgaagtttgtt-------tgcagtgcgaatct---------ttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatat----tttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
| || |||||| | || | ||| | ||| || ||| || ||| ||||| | || || || | || | || | ||||||||||| || || ||||||||||||||||| || ||||| || ||||| ||| || |||| |||||||||||| |||||| | || ||| |||| |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgac-ttgatttttttgttcttaaaatcccatatatagGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 9
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgata--tattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
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---------gttgacagtttccaaacttaaataggattttcttttatgtgattctgtacatcatt----ctgaaccaacagcttctttagGGAGAGAATAAAGGGTACCTTGTTTGCAAAAAGAAGATGGCAACATCTCCAGAAGCTTTGTGTTGCTTTTGTCCTCAGCCTTTTCGGCAGTTTGTTGAATMapped 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|29681938|gb|CB678213.1|CB678213EST: ATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAG GGAGAGAATAAAGGTTTCCTTGTTTGCAAG
genomic: ATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttg ... tatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
tgttgat putative branch site (score: 4)
tgttgatatatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT