Sequence
atgc intronic sequence ATGC exonic sequence...tgaactttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51690.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 12
-------------tgaactttaatgtgtatgaagtctcatagtcaactcat-atccaaatc-gatcaattacagacatggtttt--ttgttgatataattttttgttctct---------tcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
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gtaattcctttggtaatcctcctttttatcaaagatttcaagtctttgcttgatacatgtgagaatgaatatgcttttctttctggttgctggtatgactttttcccctttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG
upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G128914_T01 (Zea mays), 3'ss of exon 11
tgaactttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
| || ||| || || ||| ||| ||| | || | | | | | | |||| ||| || ||||||||| ||||||| ||||| ||||||||||| ||||| || ||||||||||| || ||||||||||||||| ||||||||
ttgttgttgttgttgttgttgttgcatgacacacttgagaatgaatgtgtttctttctgtttgctggtatgactttttcccttttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGCGAAAATTATTTTTTCCATGCTGGACAG
upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G128914_T02 (Zea mays), 3'ss of exon 11
tgaactttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG-------------------
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ttgttgttgttgttgttgttgttgcatgacacacttgagaatgaatgtgtttctttctgtttgctggtatgactttttcccttttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGCGAAAATTATTTTTTCCATGCTGGACAGGTAGTATGGCACCCCTTTA
upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
tgaactttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattaca--gacatggttttttgttgat--ataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
| | |||| || |||| ||| | || || | |||| | | || || | | | | | || | | | |||| |||||||| |||| |||||||||||||||||| ||||||| ||||| |||||||||||||| ||||| || ||| |||| |||
---atcacactgtgcattccttctc-cagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 11
tgaactttaatgtgtatgaagtctcatagtcaactc-atatccaaatcgatcaattacagacatggttttttgttgat--ataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
| | | || || |||| || | |||| | | | || || || | | | | | || | | ||| |||||||| |||| |||||||||||||||||| ||||||| ||||| |||||||| ||||| ||||| || ||| |||| |||
---atctcactgctcattccttctccagtgcatgtggatatttattttgcaacgatattgatattatgaggtaatcactgaagatatgcaccttactttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGAGAGAACTATTTCTTTCATTCTGGGCAG
upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------------------------------tgaac-tttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
| | || | | | | | | | || | | || | | | | ||| || | ||| ||| || |||| || ||||||| |||| ||||||||||| |||||| ||||||| ||||| ||||||||||||||||||| ||| | ||||
gtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctg-agatatagccttt-attgcta---ttttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGTMapped 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|58689182|gb|CK077869.1|CK077869EST: AAGGCTGAAGAAATTATGAATCTTGCGAAAGAG CTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCT
genomic: AAGGCTGAAGAAATTATGAATCTTGCGAAAGAGgtaagtcctt ... ctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCT
EST:
gi|218493252|gb|FG945787.1|FG945787EST: GCTATGAGGAGACTGAAAAGGCTGAAGAAATTATGAATCTTGCGAAAGAG CTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCT
genomic: GCTATGAGGAGACTGAAAAGGCTGAAGAAATTATGAATCTTGCGAAAGAGgtaagtcctt ... ctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCT
EST:
gi|25802227|gb|CA758188.1|CA758188EST: GCTATGAGGAGACTGAAAAGGCTGAAGAAATTATGAATCTTGCGAAAGAG CTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAATGT-GGC
genomic: GCTATGAGGAGACTGAAAAGGCTGAAGAAATTATGAATCTTGCGAAAGAGgtaagtcctt ... ctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAA-GTTGGC
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:
75 (upstream exon),
73 (downstream exon)
Score:
20GGATGAGCTTGCATGTTTTGCCCCTGGTATGCTGGCACTGGGGGCCTCTGGCTATGAGGAGACTGAAAAGGCTGAAGAAATTATGAATCTTGCGAAAGAGgtaagtcctt ... ctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
tgttgat putative branch site (score: 20)
ttttttgttctcttct putative PPT
ttttttgttgatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaactttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - -gtgtatg
- - - - - - - - - - - - - - - - - - - atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acagaca