Sequence
atgc intronic sequence ATGC exonic sequencegttactctccatctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g43970.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
gttactctccatctcat-catattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| ||| | | |||||||| | || | || |||| | | | | || |||| || | |||| || ||||||||||||||||||| |||||||||||||||||| ||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |
-----gtacaatcccctacatattgccgtgctttttggtgattcctcgagtt--atttactgaacactctacttacaagtccttttt-----ctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 5
gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| |||| |||||| | | || | | | | || | | | | | | || || ||||| |||| || ||||||||||||||||||| || ||||||||||||||| |||||||||||||||| || |||||||||||||| |||||||||||||||||||||||||| |
-----gtacactctcccaatattgtcatga-gttctggtgattcctcaagtt-agttgctgaatactctatgtataaatccttttt-----ctcagGATGTTGTCACAGAGAATGAGTTTGAGAAAAGGCTTTTGGCAGATGTTATACCTCCAAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 18
------------gttactctccatctca--tcatattgcaaacata-ttatcatac-tcacacagttggaat--ctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| | | | || | | || || | |||| | | | | | || | | ||| | | | |||||| |||| | | || |||||||||| ||||| || |||||||| || |||||| |||| |||||||| ||||||| |||||||| || || ||||||||||||||||| | ||||
gtgattgtttgtgcccttttgctacttacgtgtcgttccagctttgcttattagaagttattctgtcaggagagttcataaacactgtattttaaatcg-ttttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATTGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 20
-------------------------------------------------------gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaa-------tctcac-agtgctttactcttaa--attactttttccttctt-------agGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
|| | | || | | || ||| | |||| | | | | |||| | | |||| | |||| | | | || || || || || || |||||||||| ||||| ||||| ||||| || |||||| |||| |||||||| |||||||| |||||||| || || || |||||||||||||| | ||||
gtgattgttatggagttttgctactttgattgtgggagatagtgacatgacatccagtagtttgt-tccgaacttactgcttggaagttattctgttgatagagtttaatcaatttttttcacgaatgctgtgttttgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAACGACATTGGTGTTACTTTCGATGATATTGGAGCTCTTGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
-------------------------------------------------------gttactctccat--ctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| || | | ||| || | |||| | | | | | || || |||| | | || | || || || ||||||| || || ||||| ||||||||||||| ||||| || |||||||| ||||| | ||| ||||| ||||| ||||||||||||||||| || ||||
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------gttactctccatctcatcatattgcaaacatattatcatactcacacagttgga-------atctcac-agtgctttactcttaa--attactttttccttctt-------agGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
|| | | || || | || ||| | |||| | | | | |||| | || ||| | || | | ||| || || || || || || |||||||||| ||||| ||||| ||||| || |||||| |||| |||||||| ||||||||||||||||| || || ||||||||||||||||| | ||||
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgt-tcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
--------gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaat-ctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| || | || || || ||| || ||| |||||| | | | | ||| || | | | || | | || || ||| ||||||| || || ||||| ||||||||||||| || || | |||||||| ||||| | ||| ||||| ||||| ||||||||||||||||| || ||||
aagattaagatattttcg--tatattctaacacaagtat-ttagcatactggtttctctagtttatttacactgtaatggtttgaattgaattgtt--ttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
------------gttactctccatct--catcatattgcaaacata-ttatcatac-tcacacagttggaat--ctcacag-tgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| | | | || ||| ||| || | |||| | | | | | || || | ||| | || || ||| |||| | |||| | | || |||||||||| ||||| || |||||||| || |||||| |||| |||||||| ||||||| |||||| | || || ||||||||||||||||| | ||||
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattct-aaatca-ttttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 15
-------------------------------------------------------gttactctccatctcatcatattgcaaacatattatcatactca--cacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| || | | ||| | | | | | | || ||| || || |||| | | | || | || || || ||||||| || || ||||| ||||||||||||| ||||| || |||||||| || || | || ||||| ||||| ||||||||||||||||| || ||||
gtaatttaatattagatgttacaattataaacctttctccatcatattttgtggagatattttgcattactactggtatccatctagtttctttaccttgtcatgatttgaattgtggaattgtcacctgtattctttgaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCGCCAACCGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 19
gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| || || || | | | | || | | | | | | | | | || | || ||||| | || | |||||||||| || ||||||||||||||||||| || || | ||||| || ||||||| || || || || ||||||||||||||||||| ||||||
----------gtaatattatgttacttaatttctttcttcccaagctgcctagtaagttccgga--ttaagagttggtttactatactgtt-tcagGATGTTGTTACTGAGAACGAATTTGAGAAAAAACTGTTGTCGGATGTCATTCCACCTAGCGATATAGGTGTTTCCTTTGATGATATTGGAGCTCTGGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
|| | | | | |||| ||| ||| | || | | |||| | | || || | | || ||| ||| | ||| |||||||||| ||||| || |||||||||||||||||||| || |||||||| ||||| ||||||||| ||||| |||||||||||||| ||| ||||||
-gtaatttttgtaccttcatgc----aactaatttttatctttaacaagtt--------atattgattaaaa-tcaattta--tttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
--------------------gttactctccatctcatcatattgcaaacatattatcatactcacacagt-tggaatctcacagtgctttactcttaaattactttttc----cttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
| | | ||| | ||| | | || | | | |||| | | | | | | |||| | | | || | ||||||| || || ||||| ||||||||||| | ||||| |||||||||| ||||||| ||| |||||||| || ||||||||||||||||| || ||||
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAAMapped 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|58678027|gb|CK066714.1|CK066714EST: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCNNNNNNNTCACTGAAG GATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
genomic: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCAAAAAAATCACTGAAGgttactctcc ... tccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
EST:
gi|58687870|gb|CK076557.1|CK076557EST: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCNNNNNNNTCACTGAAG GATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
genomic: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCAAAAAAATCACTGAAGgttactctcc ... tccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
EST:
gi|58692889|gb|CK081576.1|CK081576EST: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCNNNNNNNTCACTGAAG GATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
genomic: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCAAAAAAATCACTGAAGgttactctcc ... tccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
EST:
gi|58659009|gb|CK047689.1|CK047689EST: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCNNNNNNNTCACTGAAG GATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
genomic: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCAAAAAAATCACTGAAGgttactctcc ... tccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
EST:
gi|29614540|gb|CB619553.1|CB619553EST: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCNNNNNNNTCACTGAAG GATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
genomic: TGCTGCAGAATATGCAAAGTGATAACAAGAGCTCAAAAAAATCACTGAAGgttactctcc ... tccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATA
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),
69 (downstream exon)
Score:
64CCTTAAGCATGGGCTCAACATGCTGCAGAATATGCAAAGTGATAACAAGAGCTCAAAAAAATCACTGAAGgttactctcc ... tccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
ttactttttccttctt CT-rich tract
tttactcttaaattac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG