Sequence
atgc intronic sequence ATGC exonic sequence...taagtaaatttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
Basic information
species | Oryza sativa |
transcript | LOC_Os09g15430.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116952_T07 (Zea mays), 3'ss of exon 2
taagtaaatttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaa--------ctgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
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-------tcttgaagaattgagtggtctgatatattg-agtcattagttttatctggaaactgaaatgaacattgtggtctgaactctgaagtgattacatattacagGCTTAGTGTGCTGGCTTATCACTTCAAGACAGGTGTTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATT
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
taagtaaatttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT-----------------------------------
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------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
taagtaaatttgaagaaatgcgtgatgcgagatc---ttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
| | | ||| | || | | | | ||| | || ||||| ||| | ||| || || | || | | || || | | |||| | || | | | | ||||| | |||||||| || || |||||| |||||||||||||||| ||||| ||||||||||| || || ||
agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaataactt--atgaagttgc-taagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 1
taagtaaatttgaaga---aatgcgtgatgcgag----atcttatagtacttagttttgtgctaaatttgatatggatgtattaactgagg-tgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
| |||||||| | || || | | | | || ||||| ||| | ||| || ||| | | ||| | || | | | |||| | || | | | | ||||| | |||||||| || || |||||| |||||||| ||||||| ||||| ||||||||||| || || ||
----cagttttgaagatttagtgttcaattcaatcatcaattcctatgacttaatttggaaataactt----atgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
taagtaaatttgaagaaatgcgtgatg--cgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
| | | ||| | | | || | ||| | || |||| | | ||| || || || | || | | | | | || |||| | | | | | | | ||||| | | || |||| || || ||||||||||||||||||||||| ||||| ||||| ||||| || || ||
tttgatattttaatgtattgtttcatgattataactttcaagtattggaatatgtaatagctt--atgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
taagtaa-atttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgcta-aatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
| || |||| | || || || || | | ||| | | | || | ||| | | | | ||| | | |||||| || |||| || | | | |||| || | || || ||||||||||| |||||||| ||||| ||||| ||||||||||| || ||| | ||
-acatagtgtttgtaaaactgtgtttctatgcatgct-ttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
upper sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 2
----taagtaaatttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacat-tacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
||| |||| ||| | | | | ||| | | | | | || || | ||| | | || | | || ||||| || |||| || | ||| | ||||| |||| || | ||||| |||||||| || ||||||||||| |||||||||||||| ||||| || ||| ||
tctgatagttaattattttaaacttttaacccttttttgtatc-cattcaataat---ttatatattgtatcggt-taatgatgtagctgatttctgatacccagGTTCAGTGGAATGGTGGACCATTTTAAGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCTMapped 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|29670629|gb|CB666904.1|CB666904EST: AGCAGTGGTACTGTTTTGCATTTTGGATGTATCACAATTTCGTGTCCAAG GCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGC
genomic: AGCAGTGGTACTGTTTTGCATTTTGGATGTATCACAATTTCGTGTCCAAGgtaatttgta ... tacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGC
EST:
gi|218500518|gb|FG959268.1|FG959268EST: TGCATTTTGGATGTATCACAATTTCGTGTCCAAG GCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGC
genomic: TGCATTTTGGATGTATCACAATTTCGTGTCCAAGgtaatttgta ... tacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
tattaac putative branch site (score: 1)
taaatttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagtaaatttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG