Sequence
atgc intronic sequence ATGC exonic sequence...attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g04980.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------attttttaggctatctattttaatt-tattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttctttt---ctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
||| | |||||| | || | || ||| || | |||||| ||| | ||||||| || ||| | | || || ||||| | | ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || ||||||
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
attttttaggctatctat-tttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattt-taattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
| | | | | | || | | | | || ||| | ||| || | || | | | ||| | | |||| | ||||| ||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | |||||||||||| ||
--caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
| | | || | || |||| | | || | | | | | |||| || || | | | | ||||| |||||||| || ||||| || ||||||||||| ||||| || |||||||| || ||||| ||| | || || | || || ||||||| || ||
---------gttttataaatcaaaacattcttgttatttctttctttgcggaagaaaaagt----tgaaatgtttgttaaaacttcaatgtgcatgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
-attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttc--ttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
||| ||| | | ||| | | | || | || | ||| | | | |||||||| ||| | || ||||||||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || || |||||
aattgcttacaaaagaaactttgtgaagagcaggaacatgccaactttaagttatgaaattttagtctcttagcgaaaattgatg--gccaacttatgaca-gGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------------------------------------------------attttttaggctatctatttta------atttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
|| | || | | ||||| || || || || || | | | | | || ||| ||| ||| | || || | | ||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| ||||||||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaa---aagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctca-agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
| | | | | |||| || | | | | |||| | || || | | | || |||| || | || | ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| ||||||||||| | | || || | ||||| | |||
-tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
--------------------------------------------------------------------attttttaggctatctattttaatttattcccctggaactctgtttc--gtctgatt--acttttcttatt----aaattttaattgatgcaattttcttttctca--------agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
| | || || | | || | | | ||| || |||| | || ||||| |||| | ||| || | | |||||| || || || ||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| ||||| | ||| ||||| |||||||||||
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATT
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttct---tttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
| ||||| || | | | || | | | || | | | | | || | | | | ||| || | ||| | | ||| ||||| ||||||||||||||||||||||||||||||||||| || || || ||||||||||| | ||| | | ||||||| ||||||| || ||
aagttttattct---tctctgaaactgtaactagaaaaaattatctggaagtggcagttcttatgctcatgtttgttttgtatcctttaatcactgtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
|| | || | | ||| ||||| |||| | ||||| | | ||||||||||||||||| ||| | || || || ||||||||||| || ||||||||||||||||||||| || ||||||| |||| ||||| || |
-----------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcatttt----ttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC
upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
|| | || | | ||| ||||| |||| | ||||| | | ||||||||||||||||| ||| | || || || ||||||||||| || ||||||||||||||||||||| ||| ||||||| |||| ||||| || |
-----------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcatttt----ttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCMapped 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|66919239|gb|CX106087.1|CX106087EST: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST:
gi|58590451|gb|CF988759.1|CF988759EST: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST:
gi|58595336|gb|CF993644.1|CF993644EST: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST:
gi|29665943|gb|CB662218.1|CB662218EST: AGGGCGTTTAANAATTATAGATAG GAAAAAGAACA-TTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: AGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
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:
72 (upstream exon),
75 (downstream exon)
Score:
10GAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
caattttcttttctc CT-rich tract
attacttttcttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
- - - - - - - - - - - - - - - ccctgga
- - - - - - - - - - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgca