Sequence
atgc intronic sequence ATGC exonic sequencegtactccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47530.2 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 22
gtactccctttatagagctatgcagagttccagattgttcac-atcttgaatactcctt---ttgctgatatc-------tgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
| | | | | | ||| | | || || |||||| | || | || |||| || |||||||| || | | | | |||||||||||| ||||| || |||||||| |||||||| ||||||||||||||||||||| |||||||||| ||||| |||||||||
---gtacttgtgcaacgttatactca--tcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacagTGGTTTGGAGAGGGAGAAAAATATGTGAAAGCTGTTTTTTCACTTGCAAGCAAAATTTCTCCTAGTGTTATTTTCGTGGATGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 5
---gtactccctttatagagct-atgcagagttccagattgttcacatcttgaatactccttttgc--tgatatctgattctga--cagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
| | ||| | | | | || | || | | ||| | | | || | | || ||| || ||||||||||| |||||||| || |||||||||||||| ||||| || || || |||||||||||||| || || ||||| || ||
gttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 17
gtactccctttatagagctatgcagagttccagattgttcacatc-ttgaatactccttttgctgata---------tctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
||| || || | | || |||| | || ||| || || | || | | | || || | ||||||||||| || || ||||||||||||||||| || ||||| || || |||||||||||||| ||||| |||||||| || |||
gtatcaatattgtaaattact------ttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 18
------gtactccctttatagagctatgcagagttccagattg--ttcacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
|| |||| | || | ||| | ||| || || | | | | | | | | | || | ||||||||||| || || || |||||||||||||| || ||||| || || |||||||||||||| ||||| |||||||| ||||||
gtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctg---atatctgattctg------acagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
||| | || || || || || | | || |||| || || | | | | || || || || ||||||||||| || || ||||| |||||||||||||| ||||| || || |||||||||||||| ||||| |||||||| || |||
gtattaatgttgta-agttacttttttttgtggtgtattt---ccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 18
------gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactcc---ttttgctgatatctgattctga--cagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
| ||||| | | ||| || || || || | || | | | || | | | | || ||||||||||| ||||||||||||||||| |||||||| || || || || || |||||| | |||||||| || ||||| ||||||
gttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
------------gtactccctttatagagctatgcagagttccagattgtt-cacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
||| ||||| | | | ||| | ||| ||| || | | | ||| | || | || ||| |||||||||| |||||||| ||||| || |||||||| ||||| || ||||| |||||||||||||| || || ||||| || ||
gttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccat-tttgcttc----agTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 18
------gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
|| |||| | | | ||| || ||| | | || | || | | | | | || | ||||||||||| || || || |||||||||||||| || ||||| || || |||||||||||||| ||||| |||||||| ||||||
gtattagttgcaaatttaaactgttttgctctactctgtattttcctttcattcattaagtgacaggatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
------gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactc----cttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
| || || | || ||| || ||| || || | || | | | ||| || ||| || ||||||||||| ||||||||||||||||| |||||||| || || || || || |||||| | |||||||| || ||||| ||||||
gttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 21
-----gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactcct--tttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
| | | || | || || | | ||| || | ||| | | | | ||| ||| | | | ||||||||| | |||||||||||||||||||||||||| ||||| | || || |||||| | || || | || ||| |||| |||
gtaacagaatatccttgaaaagt--tggactctaccaatttatacacggaatctcttgttcaaacttgtgttcttctcaatattgcagTGGTTTAGTGAGGGTGAGAAATATGTCAAAGCTGTCTTTTCGTTGGCTAGTAAAATTTCCCCAAGCATTATCTTTTTGGACGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 21
gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactcctt-ttgctgatatctgattctg-acagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
||| | || || | |||| | ||| | ||| | | | | | | || || ||||||||||| ||||| ||||| || || |||||||| || || | || ||||| ||||| || |||||||||||||| ||||||
gtaactctcataaagtgatatgatttccttttatgctttcttttaatgattgtacttgaccatttacactaaatgctttgcagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 21
------gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
| | | || | | || | | | || || || | | | || | ||| | || | | || ||| ||||||||||| ||||||||||| |||||||||||||| ||||| | || || ||||| | ||||| || || |||||||| |||
gtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttctt----cttaatactg-cagTGGTTTGGTGAGGGTGAGAAGTATGTCAAAGCTGTCTTTTCTTTGGCCAGTAAAATGTCCCCTAGCGTTATCTTTGTGGACGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
----gtactccctttatagagcta--tgcagagttccagattgt---tcacatcttgaa--tactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
|| | | | | | | | || || ||| || | ||||| || | | ||||||| | || ||||||||||| || || ||||||||||||||||||||||| || || || || |||||||| |||||||| ||||||| || |||
gtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatat----tgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG
upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 22
--------------gta-ctccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctgatatctgattctg------acagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
||| || | ||| | | | | | | || ||| || || | | | |||| | ||| || | ||||||||||| ||||| ||||| ||||| || || || || |||||||| || ||||||||||||||||| | |||||||||||
gttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttattttt--ttttttctcagctggtttctcatctttcttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAAMapped 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|29664460|gb|CB660735.1|CB660735EST: AGGCTGGCGCCAATTTTATCAACATATCAATGTCTAGTATTGCTTCAAAG TGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGC
genomic: AGGCTGGCGCCAATTTTATCAACATATCAATGTCTAGTATTGCTTCAAAGgtactccctt ... attctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGC
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:
73 (upstream exon),
71 (downstream exon)
Score:
51TGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATATCAATGTCTAGTATTGCTTCAAAGgtactccctt ... attctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttccagattgttcacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
ttgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA