Sequence
atgc intronic sequence ATGC exonic sequencegtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 5
gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcg--taacttcttcctg-tagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
| | | ||| || | | | || | || | | | || | || | || ||||| ||| ||||| ||||||| |||||||||||||| ||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||
------------------gtccttggatcatttctttcatagtctttgatgcaataaatttgcttgtattattaaattacattcttactggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcg--taacttcttcctg-tagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|||| ||| || ||| ||| | | | | | | | | ||| || | || ||||| ||| ||||| |||||||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||||
-------------gttcttggatcactta--tttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
-gtgcttatacaagtttctctagtcaattggttttct---ttacatattctgcag-tcattactctaattattttgctcgtaacttctt----cctgt-agATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|||| | || | || | | | |||| | || | || || || | || || | || || || |||| |||| ||||||| || || ||||| ||||||| ||||||||| | ||||| || |||||||| || ||||||||||| || |||||| | ||||| ||||
ttagcttttctttgtggttttaat-ggtagattttaggagtagtgtaaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
--------------------------------gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcatta-ctctaattattttgctcgtaacttct--tcctgt-agATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|| || | || || | | || | ||| || |||| | | ||| | | | | | ||| | | | ||||| ||||| ||||||| || || |||||||||||||| ||||||||| | |||||||| |||||||| || ||||||||||| || ||||| || || || ||||
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattg-gtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
-----------------------gtgcttatacaagtttctctagtcaatt-ggttttctttacatattctg-cagtcatta-ctctaattattttgctcgtaac-ttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|| | | |||| | | |||| | | | | | || | || | ||| | | | | || ||| | | || || ||||| ||||||| || ||||||||||||||||| ||||||||| | ||||| || |||||||| || |||||||| || || ||||| || || |||||||
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
-------------gtgcttata-caagtttctctagtcaatt-ggttttctttacatattct------------gcagtcattac--tctaattattttgctcgtaacttcttcctg-tagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
||| | || | || || | | |||| || | ||| || || | | ||| |||| | |||| |||| | | | |||| ||||| ||||||| || || ||||||||||||| ||||||||| | ||||| || || ||||| || ||||||||||| || |||||| | ||||| ||||
gttatctgtctttttgcatgtaacttattgttcaacttaattcgggtgccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgcttatacaagtttctctagtcaattggttttcttta--catattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|| | || || || | || ||| | | | || || | || | | || | | | ||| | |||| |||||||| || ||||| |||||||||| |||||||| ||||||||||||||||||| | || || | || || ||||| ||||| || || |
gta-taatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgcc--agATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
gtgcttatacaagtttctctagtcaattg----------gttttctttacatattctgcagtcattactctaattattttgctc--gtaacttc----ttcctg---------tagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|| || | | | | | |||| || | | | || ||| | | | || || ||||| | |||| | || || |||| |||| || || || |||||||||| ||||||||||||| | |||||||| |||||||| || |||||||||||||| ||||| |||||||| ||||
gtatttttttagccctgtttggtcagatgacgcattcctgctctgttctcatgtgcccttatatatatgtaaaacattttattatggtaatctaaggatttttggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
----gtgcttatacaagtttctctagtcaattggttttctttacatattctgca--gtcattactctaatt----attttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
| |||||| | | || | | ||| | || | ||||| |||| || | || || || | | | | ||||| |||||||||| || ||||||||||||| |||||||| | ||||| |||||||| ||||| || || ||||||| ||||| ||||| || || |
actccttggtatacatcagtgttatgtagaataacttt-tatagttgcactgcatcgtcagtagcatcatatgtgatgctgaccaatggtcgtgtgtttagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------gtgctt---atacaagt--ttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcgtaacttctt---cctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
| || |||| ||| || || | || | | || | | || | | | || | | ||| | ||| | | || |||| |||||||||| |||||||||||||| | ||||||||| | ||||| |||||||| ||||||||| | |||| || ||||| || ||||| || |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------gtgcttatacaagt-ttctctagtcaattggttttctttacatattctgcagtcat-tactctaat-tattttgctcgtaacttcttc---ctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
|||||| | | | | ||| | | || || | | | | ||| | ||| | |||| ||| ||||| ||| |||| |||||||||| || ||||||||||| | |||||||||| | |||||||||||||| ||||||||| | | || || ||||| || ||||| || |
gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttcgcagaatatattttttcgtacacaaatgtgagatgcttctaatttcttagaactgcagATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 5
gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
| | || | || ||| | | | | || || | | ||| ||||| |||| ||||| || | ||| || || ||||||||||| |||||||||||||||||||| || || ||| ||||||| || || |||||||| || |
-----------------------------------gtaatattagcctgggtgattttttttaattttctggccctcctttcgctgcatagATTTTGAAAGAGCTCCACAGATCGTGCCAGAGAGAAGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 5
gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
| | || ||| || ||| ||||||| | | | | | | |||| ||||| |||| ||||| || | ||| || || ||||||||||| |||||||||||||||||||| || || ||| ||||||| || || |||||||| || |
----------------------------------gtaatcttagcctg-ggtgatttttctaattttctgacccttca-ttctctgcatagATTTTGAAAGAGCTCCACAGATCGTGCCAGAGAGAAGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGAMapped 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|6431605|gb|AU081257.1|AU081257EST: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAG ATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
genomic: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAGgtgcttatac ... cttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
EST:
gi|55827482|gb|AU032236.2|AU032236EST: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAG ATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
genomic: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAGgtgcttatac ... cttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
EST:
gi|3107821|gb|D43561.1|D43561EST: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAG ATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
genomic: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAGgtgcttatac ... cttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
EST:
gi|86532861|gb|CI173067.1|CI173067EST: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAG ATACTGAAGGAGCTGCATAAATCTTGCCAAAGAGAAGATGGTTCTGATGAT
genomic: AGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAGgtgcttatac ... cttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGAT
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:
37AGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAGgtgcttatac ... cttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacatattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
tcgtaac putative branch site (score: 37)
cttcttcctgt CT-rich tract
attactctaattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC