Sequence
atgc intronic sequence ATGC exonic sequenceTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os11g01380.1 |
intron # | 28 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag------------
||| ||||| ||||| || ||| ||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||| | || ||| || ||||| || | |||||| | |||| ||||| |||| || | | ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 26
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag------------
||| ||||| ||||| || ||| ||||||| | ||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||| |||||| | || ||| || ||||| || | |||||| ||||||| ||||| |||| || | | ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagtttaccatagtaacatctctactgtgctatgtgactgtgtgcgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag
||| ||||| ||||| || ||| ||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||| | || || || ||||| | | |||||| ||||||| ||||| |||| | | || ||| ||||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatc-cctactatgtgcgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 5
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttccgttcatgtgtt-tgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag
||| ||||| ||||| || ||| ||||||| ||||||| |||||||||||||| ||||||||||||||| |||||||||| ||||| || ||||| |||||| ||| ||| || ||| | | || | || |||| | | | ||| | || |||| | |||| |||||||||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatc-catgctgcgtgtgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatct----tgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttg--cttcgtgtgcag
|| ||||| ||||| || ||| ||||||| ||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| || ||||| |||||| || | |||| | | | | ||| | || ||||| | ||||| | || || || || |||||||||
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 12
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag------------
||| ||||| ||||| || ||| ||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||| | || ||| || ||||| || | |||||| |||||| ||||| |||| || | | ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag------------
||| ||||| ||||| || ||| ||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||| | || ||| || ||||| | | | |||| |||||| ||||| |||| || | | ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtctgcgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 27
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag----------------------------------------
||||| ||| |||| ||||| |||||||| || || ||||||||||| | || ||||||||||| ||| | |||||||| ||||| ||||| | ||||| |||| | | ||| |||| | || || | |||| || | | | || | || ||| |
GTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAGTTGGCCTGGATGAACAATATGATTGACTTTGCCTTCCCATATCTCCTGCAGgt---ttgtattccttc-tgtgctgcttacctttattacttaaacatacatcgacatgtatgtctttttcatcatgttatgtagtgcgttctttcactatcttcttttttcgctgttgtag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 28
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtat---cttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaac----aaagcttgcttcgtgtgcag
|| |||||| | |||||||| | || || | ||||||||||||||||| | ||||||||||| ||| | || ||||| || || ||||| |||||||||| |||||| | | || | || || | | || | |||| ||| || ||| || || || || ||
ATGCCTCTTTGTCTGTTATGATATTATACGGCCAGATGTTGCTCTTGAGCTATCTTGGATGAACAATATGATTGATTTTGCTTTTCCATATCTCTTACAGgtatgtatttgtttgtggttatat-ttatcaacagatgaaatatattctttttttgctaaaaattttgaaatgtttttttgtttgaag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 28
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag-----------------------------------------------------------------------------------
||| ||||| | |||||||| | || || | ||||||||||||||||| || ||||||||||| ||| | || ||||| ||||| || || |||||||||| || | || | | ||| | | | | | ||| || | || | ||
TTGCCTCTTCGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttcccctggggtttcttttttttatgtgaaatggggctaaaagcccaaggaaaagagactaaacaggaatgacacgaggggtttctttcgctatatgtattactggatgatttttcttccttttattgataaccattttttaatatttcccccctag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 28
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtat---cttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaac----aaagcttgcttcgtgtgcag
|| |||||| | |||||||| | || | | ||||||||||||||||| || ||||||||||| ||| | || ||||| || || ||||| || ||||||| |||||| | | || | || || | | || | |||| ||| | ||| | || || || ||
ATGCCTCTTTGTCTGTTATGATATTATATGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTTCCATATCTCTTGCAGgtatggatttgtttgtggttatat-ttatcaacagatgaaatatattctttttttgctaaacattttgaaatttatttttgtttgaag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 26
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccat------aacaacaaagcttgcttcgtgtgcag-------
||| |||||| | |||||||| | || || | ||||||||||||||||| || ||||||||||| ||| | || ||||| ||||| || || |||||||||| || | | | | || |||| ||| | | |||| | | || | || || || | |
TTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttccactggggtttcgttcactatatttattactggatgatttttcttccttttaatgataatcattttttaatatttcccccctag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttc--cgttcatgtg----tttgggactattcatttac--------gaacagttttccata----acaacaaagcttgcttcgtgtgcag--------------
||||||||| | ||||||||||| ||||| | || || ||||| || ||||| ||||| ||||| ||| |||||||||| ||||| ||||| | ||||| | | | ||| | || || | | | | |||| || | | | | || | | || |
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttcc--gttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag--------------------
||||||||| | ||||||||||| ||||| | || |||||||| || ||||| ||||| ||||| ||| | |||||||| ||||| ||||| | |||||| || | | | | | | ||| | | | | || | || | ||
ATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACTTTGCCTTCCCGTATCTCCTCCAGgtaatttatcctccaatccctaaaataccctctacctgatgagataggaaccatactgacgctatgatcaactctctttgatcccgtcattttttcttcacag
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgttt---ccgttcatgtgtt-tgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag
|| |||||| | ||||| || || || || | || |||| ||||||||||||||||||||||| ||| | |||||||| ||||| ||||| ||||||||| | ||| | | ||| | | | || | | | || ||| | ||| || | | || | ||
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcat-tttttttcatagMapped 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|87030226|gb|CI270236.1|CI270236EST: CTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: CTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29685119|gb|CB681394.1|CB681394EST: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAACGACATGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29627717|gb|CB632728.1|CB632728EST: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29626374|gb|CB631385.1|CB631385EST: CATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: CATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29624173|gb|CB629184.1|CB629184EST: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
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:
191TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA