Sequence
atgc intronic sequence ATGC exonic sequence...gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40830.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 7
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA----------------------------------
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-------------cttgcctctta------gctagtactttt----ttttggttatataatctcagcac-----------cagaaccaatacctgtacaggtcgctgctgccaaagcagatttgaactatattgGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTATAAAGTTGCATGGTGGTACGCCCGCCAATTTTCT
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------gaggatggcttgacttgcctctggagggatgttac----agcttttgttgttctgagaatggaaactgaagatatttatgagtttatctcta------atacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
| | ||||||| | | | | || | || ||| | | | | | | | | ||| | | | | | | |||||| ||||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||| || ||||||||||| ||||| || ||||| || |
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggt-tatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
-gaggatggcttg-acttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
| | ||| |||| | | || ||| | | || |||| | | | || || | | || | || | ||||||| ||||||| || || || || || || |||||| | |||||||||||||||||||||||||| || ||||| || |||||||| |||||||| || |
catgatctgtttgtgcttgattattaag--cccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 8
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatgga--aactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
|| | |||| | | || ||| | | || | |||| | | || || | || | || | | | ||||||| ||||||| || || ||||| || || |||||| | ||||||||||| |||||||||||||| || ||||| || |||||||| |||||||| || |
ttatctgtttgtgcttgattattaag--cccttatatccttgaatcttctttttttttactgggtgtgtgtaacattatgtgtgccttttaactttgaacagGTGACTGCTGCAAAGGCAGACTTAAATTATATTGGGTTAGATGGAGAAATAGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagttta-tctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
| || | |||| | | | ||||| || ||| | | ||| || | | || | | | | || | ||||||||||||| |||| |||| |||||||||| || | |||||||| ||||| ||||||||||| ||||| |||||||| ||||| || ||||||||||
------gtctctgtctatctcttgta--tcatcaagaaagccattgttatgttaattcgat---aggatgttaaaaggaatagtgtgttgtgtctc-atagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------------gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatg-gaaactgaaga----tatttatgagtttatctctaataccttt-----acagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
|| | || | | | | | | || | | | || | ||||| |||| ||| || | ||| | | | | | | ||||||||||||||||||| || ||||||||||| || | |||||||||||||| ||||||||||| ||||| || || ||||||||||| ||||| || |
gttgggttacttcttttaatttcttgaccctgttttatctgtgatgtaagtggaaagtagcacatgtacataccataaaggcaatccccctctcttcacaactacaaggtaaaactaaagaacaatatgtaatgttctatttgtggtttcactgtacaatagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatattt--atgagtttatctctaatacctttac---agGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
| || |||| ||| | | | | | | | || | | | ||| || | | || ||| || | | || | |||| ||||||| || | ||| |||| ||||| || | ||||| |||||||| ||||||||||| || || || | ||||||||||||||||| ||||
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacga-agattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
| ||||| | | | || | | || || || | |||||| |||||||| || || |||||||||||||| | ||||| || ||||||||||||||||| || |||||| | || ||||| || ||||| ||||
----------------------------------------------gtttgagaccttgttc---atagtttcacgttttaatgcctgttcgaaaaacagGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCAMapped 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|58589675|gb|CF987983.1|CF987983EST: CAGGAAGATCCCAGAGAG GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: CAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST:
gi|218478127|gb|FG953382.1|FG953382EST: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST:
gi|66913068|gb|CX099916.1|CX099916EST: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST:
gi|163921201|gb|EG714126.1|EG714126EST: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST:
gi|163929534|gb|EG713477.1|EG713477EST: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG GTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATT
EST:
gi|13420568|gb|AU174658.1|AU174658EST: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAG GTGGCTGCTGCCAAAGCTGACTTGAACTAC
genomic: AGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTAC
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),
68 (downstream exon)
Score:
33GGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTGCCATGCGTGACACAACACAGGAAGATCCCAGAGAGgtatattact ... acctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
ctctaat putative branch site (score: 33)
taccttt CT-rich tract
atatttatgagtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
- - -tggcttg
- - - - - - - - gcctctg
- - - - - - - - - - - - - - - - tacagct
- - - - - - - - - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -aatggaaa