Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttctagttgttcgtcaatatattcttgaatgttcatgtttaattagctcagttaatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11140.2 |
intron # | 5 |
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 5
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 5
gtaagttttctagttgttcgtcaatatattctt--gaatgttcatgtttaattagctcagtt----aatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
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gtaagtatctaatgcagttccaatttttttctttaaaatgttctcgtctggttttctcagtttcttaattgattcaatttgttcctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 5
gtaagt-tttcta----gttgttcgtcaatatattcttgaatgttcatgtttaattagctcagttaata-tga-tatttttctttcta--ttacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
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gtgagtatctctgaaatgttgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagcgactctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATTGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 5
gtaagttttcta------gttgttcgtcaatatattcttgaatgttcatgtttaattag---ctcagttaatatgatatttt-tctttct--attacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
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gtaagtccttgaaattatgtcagatatgaatacaattgtatactttgtagttgattttgactttcagttgctgtgctaatctgtttttctgaattccagCATGACCACCGAAATGGTTGCTTGTATTGCCATTGAAGCAATATCTATATTGGAAAAAATGCACTCTCGAGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 5
----------gtaagttttctagttgttcgtcaa--tatattcttgaatgttcatgtttaattagctcagttaatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
| || | | || | | | || | ||||||| ||| || || | || | | | || | ||| | | ||| ||| ||| | ||||||||||||||||||||| || |||||||| || |||||||| || ||||| || |||
gtaagtccttgaaattatgtcagatatgaataaaattgtattctttgtagttgattttgactttcagttgctgtgctaatgtgtttttctgaattccagCATGACCACTGAAATGGTTGCTTGTATTGCCATTGAAGCAATATCTATATTGGAAAAAATGCACTCTCGAGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
---------------gtaagttttctagttgttcgtcaatatattcttg--aatgttcatgt-----ttaattagctcagttaatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
| | | | | ||| || |||| || |||||| | || | ||||| | || | | ||| ||| || ||| |||||| |||||||||||| |||||||| || || || ||||||||||| |||||||||||||| | |||
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 5
---------------gtaagttttctagttgttcgt------caatatattcttgaatgttcatgtttaattagctcagttaat---atgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
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gtgagtgagatgaaaatatgatttattattttttatatgctacaaatggttctgttgcttttaccattttgtgcttgtatttgcctaatgaagatatttgcttaattccagTATGTCCATTGAAATGGTTGCATGCATTGCTATTGAAGCAATATCCATATTGGAGAAGATGCACTCCAGAGG
upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttttct----agttgttcgtcaata-------tattcttgaatgttcatgtt-------taattagctc--agttaatatgatatttttctttct--attacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
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gtaagtttctttttcaaatatgtggcggaaagtgtgttatcttttagtttatatgtaacacatgcaatttactcttatctaatgtttactttcactttgtcaatttcagGATGTCCATTGAAATGGTAGCATGTATTGCTATTGAAGCAATCTCTATATTAGAGAAGATGCACTCTAGAGGMapped 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: GACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTC AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATT
genomic: GACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTCgtaagttttc ... tctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaatgttcatgtttaattagctcagttaatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
agttaat putative branch site (score: 4)
tatttttctttctatt putative PPT
agttaatatgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttctagttgttcgtcaatatattcttgaatgttcatgtttaattagctcagttaatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG