Sequence
atgc intronic sequence ATGC exonic sequencegtatttcttattacaatgattttctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g55600.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 5
gtatttcttattaca--atgattt-tctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
||||| |||||| | || | |||| |||| ||||||| | | |||| | | | | || ||| || | | | | ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||| || ||||| |||||||| || || || || || ||||| |||
gtattagttattatatagtggcatatcttccatcctattgttactgtttactcataccatgcattgagttgagctgcctttttattcttattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAACACACTTCTAGATGGGAGTGACGCTCCTCGCTTGAAGATTTGCGATTTCGGTTATTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 4
gtatttcttattaca--atgattt-tctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctactttctcc-attttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
||||| || ||| | ||| | ||||||| ||||||||| | |||| | | | | |||||| || | | || || ||||||||||||||||||||||||||||||||| ||||||| ||||| || ||||| || |||||| |||||||| ||||||||||| || ||||| |||
gtattagttgttatataatggcacatttttcatcatattgttattgtttactcataccatgcattgagctgagctgccttttttattcttattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G138861_T03 (Zea mays), 3'ss of exon 4
---------------------gtatttcttattaca--atgattt-tctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
||||| |||||| | || | |||| |||| ||||||| | | |||| | | | | || ||| || | | | | ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||| || ||||| |||||||| || || || || || ||||| |||
gtaagctactgccattcaatggtattagttattatatagtggcatatcttccatcctattgttactgtttactcataccatgcattgagttgagctgcctttttattcttattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAACACACTTCTAGATGGGAGTGACGCTCCTCGCTTGAAGATTTGCGATTTCGGTTATTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 4
------gtatttcttat-tacaatgattttcttt--catctgattgttattctgtactaaggcatcgtgg------taagctgaactatcctactttctccattt--tcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
| ||| | | | | || ||| || | ||| | | | | ||| | | || | | |||| | || || ||| | |||||||||||||| || || ||||||||||| || ||| || ||||||| || |||||||| || ||||| || ||||| ||||||||||| |||
gtacatgaattcaacacatgtagtctttacttttaccagttatttgcttcccagaagaaagaaagcatgagatgtctgacttgaatttctatatttgtcttctttaatgaagCAAGTATGCCATCGCGACTTGAAGTTGGAAAACACATTGTTGGATGGTAGTCCTGCTCCTCGTTTGAAGATTTGTGATTTTGGCTATTCAAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 4
----gtatttcttat-tacaatgattttcttt--catctgattgttattctgtactaaggcatcgtgg------taagctgaactatcctactt--tctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
| ||| | | | | || ||| || | ||| | | | | ||| | | || | | |||| | || || ||| | | |||||||||||||| || || ||||||||||| || ||| || ||||||| || |||||||| || ||||| || ||||| ||||||||||| |||
gtatgaattcagcacatgtagtctttacttttaccagttatttgcttcccagaagaaagaaagcatgagatgtctgacttgaatttctatatttgtcttccttaatgaagCAAGTATGCCATCGCGACTTGAAGTTGGAAAACACATTGTTGGATGGTAGTCCTGCTCCTCGTTTGAAGATTTGTGATTTTGGCTATTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 4
gtatttcttattacaatgattttctttcatctgattgttattctgtacta-aggcatcgtggtaagctgaactat---cctactttctccattt--tcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
|||| | | || | | | ||| ||| ||| | ||| || || ||||| | ||| || |||| | |||||||||||||| ||||| |||||||||||||| ||| || ||||||| || || ||||| || ||||| || ||||| ||||| ||||| |||
----------gtaca-taagttcggcatctttagtctttactct-tacaataggtataatgagttgctgacttgaatgtctatttatcttatttaataaagCAAGTATGCCATCGTGACTTGAAGTTGGAGAACACATTGTTGGATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCAAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 4
gtatttcttattacaatgattttctttcatctgattgttattctgtactaag-gcatcg---tggtaagctgaactatcctactttctccattt--tcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
|||| || || | | | | || | | || | | | || | | | || | ||| || |||| | |||||||||||||| ||||| |||||||||||||| ||| |||||||||| || || ||||| || ||||| || ||||| ||||| ||||| |||
----------gtacataagttcggcatctttagtctttacttttacaataggtataatgagttgctgacttcaatgtttctatttatcttatttaataaagCAAGTATGCCATCGTGACTTGAAGTTGGAGAACACATTGCTGGATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCGAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatttcttattacaatgattttct--ttcatctgattgttattctgtactaag-gcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG-------
| | | || || | || | | ||| || || | | | | | | || | | | | | | |||||| ||||||| || ||| ||||| |||| |||||| || | |||||||| || || || || |||||||||||||| ||||| ||||| |||
---gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttcttattacaatgattttct--ttcatctgattgttattctgtactaag-gcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
| | | || || | || | | ||| || || | | | | | | || | | | | | | |||||| ||||||| || ||| ||||| |||| |||||| || | |||||||| || || || || |||||||||||||| ||||| ||||| |||
---gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 4
------gtatttcttattacaatgattttctttcatctgattgttattctgtactaaggcatcgtgg----taagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
| || | || || | | | | ||| || ||| | || | | || |||| || | | | | | |||| |||||||||||||||||||| ||||| |||||||| |||||| | ||||||||||| ||||| || ||||| || ||||||||||| || || |||
gtattcaaacttttagttttctgccttaacctctgttttattatttgcctgaaaaaaatgaactaggcgattaagttggatttcatgttgtatttctttttgaagCAAGTATGCCACCGTGACTTGAAATTGGAGAACACACTGTTAGATGGAAGCCCAGCTCCTCGTTTGAAGATTTGTGACTTTGGGTACTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 4
------------gtatttcttattacaatgattttctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctacttt-ctccattttc------aagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
| ||| || | | || | |||| | | | || | | | ||| || | | | | |||| ||||| || ||| | |||||| |||| ||||| || ||||||||||| ||||| || ||||||||||||| |||||||| ||||| |||||||| ||||| || || |||
gtatttgagcttttcttttttctgaaaaaaaaaatcttgaaaatttgtattcctttattctacta-attccaattatataatttatctgacttttctatattcttttgatgaagCAAATATGTCACCGGGACTTGAAGTTGGAAAATACTTTGTTGGATGGAAGCCCAGCTCCACGTTTGAAGATATGTGATTTTGGGTACTCCAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gtatttcttattaca-atgattttcttt----catctgattgttat---tctgtactaaggcatcgtggtaagctga--actatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
| | | | || ||||| | ||| | | || | | ||||| | || || | | | |||| || || | || |||||| ||||| | || |||||||||||||| |||||||| ||| ||||||||||||| ||||| || | ||||||| ||||| ||||| ||||| |||
gtaattgttctgaaccctgacgcgcgtggttttcctatcagcattgaagttttctggatttgtac-agtgcttccttatgacctgactacaatttttctggtaacatttt--agCAAATTTGTCACCGTGATTTGAAATTGGAGAACACATTGCTGGATGGAAGTCCTGCACCTAGACTGAAAATCTGTGATTTTGGATATTCAAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtatttcttattacaatgattttctttcatctgatt-----gttattctgtactaa---ggcatcgtggtaagctgaactatcctactttctcc--attttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
|| ||| |||| | || | | || ||| | | |||| | | | | | | | | ||| | || | |||||| ||||| | |||||||| ||| ||||||| ||||| || |||| ||||||||||| ||||| | ||||||||||||| ||||| ||||| |||
gtgatttcctgaccctttaagtatcgcaatcttattttatgatttgagttatcgggtattttctttcggtttgttcttttcctcactctgattatgcatctgcatgtgaattttccagCAAATCTGCCACCGAGATCTGAAGTTAGAGAACACGTTGCTTGATGGAAGCCCAGCTCCTAGGCTGAAAATATGTGATTTTGGATATTCGAAG
upper sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------gtatttcttattacaatgattt-tctttcatctgattgttattctgtact-aaggcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
|||| |||| | || | ||| ||||| || | || | ||| | | | | ||| || || || ||| |||| | ||||| || |||||||||||||| ||||| |||||||| |||||| | ||||| | ||||||| ||||| ||||| ||||| |||
gtattactctaatccttgaaattttagattatgtccagaaatcggctacctggactttatttagttttcaattcctcgctcttatc---aatattctgctcgtggttttctca-gCAAATCTGCCATCGGGATTTGAAGTTGGAAAATACTCTGCTGGACGGAAGCGCCGCTCCTAGGCTGAAAATCTGTGATTTTGGATATTCGAAGMapped 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|58678161|gb|CK066848.1|CK066848EST: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATG CAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
genomic: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATGgtatttctta ... cattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
EST:
gi|58693720|gb|CK082407.1|CK082407EST: CTACTGCCATTCAATG CAAGGTATGCCA-CGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAG
genomic: CTACTGCCATTCAATGgtatttctta ... cattttcaagCAA-GTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAG
EST:
gi|6117750|gb|AU081021.1|AU081021EST: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATG CAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
genomic: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATGgtatttctta ... cattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
EST:
gi|27334413|gb|CA882864.1|CA882864EST: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATG CAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
genomic: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATGgtatttctta ... cattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
EST:
gi|32948449|gb|BP185021.1|BP185021EST: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATG CAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
genomic: GCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATGgtatttctta ... cattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGC
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:
54 (upstream exon),
74 (downstream exon)
Score:
40GCTCGCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATGgtatttctta ... cattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgtactaaggcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
ctatcctactttctcc CT-rich tract
attttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcttattacaatgattttctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG