Sequence
atgc intronic sequence ATGC exonic sequence...gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g07740.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 4
gccattcacctcttaggatt-attgctttggtgtgaagctct-tatacaatat-gtgtg-ctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
|| | |||| ||| || | | || | | ||| | | ||| | ||||| ||| | |||||||||| ||||| | | | || |||||| |||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||| || ||||||||||||||||||||||||||
--tatatattatttagcatttgctgatcaaaggcgaggaattatatgttgtgtcatgtaacccttgtgcaccatgtgttgacttt-gtttcat-tcaaattaagGGCCTATGGAAGCGGAAAAGAAGATAGCCCTCTATGTGATGTGCCTGGATTTGAAAACACTAGAATGAAACTCCTGAGACATGTTTCTTTTGTTGATTGC
upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 4
gccattcacctcttag-gattattgctttggtgtgaa--gctcttatacaatatgtg-tgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
||| | | || ||| | | | | | ||| | | | || || ||||||||| | |||||| | | ||||| | ||| || |||||| |||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||||||
--tatttagcatttgatgatcaaatgtgaagaattatatgctgtgtcatgactcatgacgcccttgttcaccatctgttgattat-gtttcatttta-attaagGGCCTATGGAAGCGGAAAAGAAGATAGCCCTCTATGTGATGTGCCTGGATTTGAAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGC
upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgact--ttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
| |||| ||| | || |||| || | | | | || ||| || || | | | ||| | |||| ||||||||||||| ||||| |||||||| ||| ||||||||||| || |||||||||| | |||||| | |||||||||||||| ||||| ||||||
--------------gtgggtatttattttacattt-gccattatg----atatcagattatcttaacttttggtgaggtgatcaatttttttctaca----gGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 4
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
| |||| |||| ||| || |||| || | ||| | |||| ||| | | | || || |||||||||||||| ||||| |||||||| ||| ||||| ||||| ||||||||||||| | |||||| | || || |||||||| ||||| ||||||
--------------gtgggtatttatttg-tgt---gccattatgttat-----caagttagtttaacttttggtgagct-gatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGACGTGCCAGGGTTTGAAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGT
upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 3
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
| || || | | | | | ||| | |||| || | || ||||| || | | |||| || |||| |||||||| ||||| |||||||| |||| ||||||||||||||||||||||||| ||||||||| | || ||||||| || ||||| |||||
gtagggtgatgtctaatatatatatatatatatatatatct-gtttttcatgttaacttcaggcttttcattgttatattcaaaatattattgca----gGGCCTATGGAAGTGGAAAGGAAGATAGTCCTCTCTGTGATGTGCCTGGGTTTGAAAACTGCAGGATGAAGTTGCTACGACATGTGTCCTTTGTAGATTGC
upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
|||| | || ||| | ||| | ||| || | | || || ||||| || | | | || || |||| |||||||| ||||| |||||||| || | ||||||||||||||| ||||||||| ||||||||| | ||| ||||||| |||||||| |||||
------------gtaggttgata--tttaat-tgatacatctattttttacattaatttcagtcttttcattgttatattcaaaatgttgttgca----gGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGCMapped 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|428712|gb|D24864.1|D24864EST: AAAATCTACAAATGTGAAGACGAGAAATGTCCACGACCAATGTGCTACAA GGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTT
genomic: AAAATCTACAAATGTGAAGACGAGAAATGTCCACGACCAATGTGCTACAAgtatgcaaac ... ttacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTT
EST:
gi|58667419|gb|CK056105.1|CK056105EST: AAAATCTACAAATGTGAAGACGAGAAATGTCCACGACCAATGTGCTACAA GGCTTATGGAAGCGGGAAAGAAGACAGCCCTCACTGTGATGTGCCTGGGTT
genomic: AAAATCTACAAATGTGAAGACGAGAAATGTCCACGACCAATGTGCTACAAgtatgcaaac ... ttacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
47 (upstream exon),
75 (downstream exon)
Score:
26AGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGCTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGTCCACGACCAATGTGCTACAAgtatgcaaac ... ttacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
tgttgac putative branch site (score: 26)
tttcctatt putative PPT
tattacataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- cattcac
- - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - tgaagct