Sequence
atgc intronic sequence ATGC exonic sequencegttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 10
gtt--ttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtt----tcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
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gttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 10
gtt--ttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtt----tcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
||| | |||||||||||||| |||| || |||||| | ||| | | || | |||| | |||| |||||| |||| ||||||||||| || ||||| || || |||||||||||||||| |||||||||||||||||||
gttgcctttgttcaccatgctattatgatgtaaacttagtaagcttgttataaggtttctctgtggtccttaattgtttcattttttagATCGCAGATGGTGATCGGTTACCATTGGCCGTGAAGGAGTTGGGAAGCTGTGATCTTTATCCACAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 10
----------------gttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
|| | || || | ||||||||| || | |||| ||| | || | | | | | ||||| ||||||| ||||| || | |||| || ||||| ||||||||||| ||||||||||| |||||||||
gtatgggctcatttttacctttttttatccgt-ctaatatgtaagcaaaagtggaaacttgctttagtgacacatgc----aagtactatgttttttagATTGCTGATGGAGAAAGGCTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCACAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
--------------gttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
| || || | |||||||| || | |||| ||| | || | | | || | ||||| ||||||| ||||| || | ||||| || ||||| ||||||||||| ||||||||||| ||||| |||
gtatgggctcatttttaccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgc----aagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 10
----------------gttttctgttcaccatgctaatatgt---tgaaaacttgtaatactttcttatacgtcatgtttccta-acctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
|| | || | | |||| || | || | ||| | |||| | || | | | | | || | || |||| || || || | ||||| |||||||| ||||||||||| ||||||||||| || || |||
gtatgggctctattattcatttttttggctgta-taatttgcgagcaagaagtgttaagttctctttatttttagtgagatgtgtaagtactatgcttcttagGTTGCTGACGGAGAAAGGTTACCTTTAGCTGTTAAGGAGTTGGGCACCTGTGATCTCTACCCCCAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 10
----------gttttctgttcaccatgctaatatgttgaa--aacttgtaatactttcttatacgtc--atgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
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gtacacgccatacttgtaactcttatactgtggcataggatgacctatttgttttttgtttttcgcctgatgataagtt-tttgttctgtaacttagGTTACTGATGGAGAAAGGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 10
-------------------gttttctgttc-accatgctaatatgttgaaaacttg--taatactttcttatacgtcatgtttcctaacctgt---tctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
| || | ||| |||| || | | ||| || | ||| | | | | ||| || | | | ||| | | || | | ||||| || | | ||||| |||| || |||||||| |||||||||||||||||||||
gtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaagctttcatctctctaccttagGCTACTGATGGAGAAAGACTTCCCTTGTCTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
----------------gttttctgttcaccatgctaatatgttg--aaaactt--gtaatactttcttatacgtcatgtttcctaacctgttctatttt-tcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
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gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttcttt-cttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgttt--cctaacctgtt---------ctatt--tttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
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gtttatttccctacatgtgcagatttcatctttttggctgagatggatgagaaactattttttctcttctttttgctttgtctaacatagtcaatttggtaacatctattattctcagGTTACAGATGGAGAAAGATTGCCTTTGGCTGTGAAAGAGTTGGGAACCTGTGACCTTTATCCTCAAMapped 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|88299886|gb|CI579947.1|CI579947EST: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAG ATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctgtt ... tatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
tcctaac putative branch site (score: 1)
cctgttctatttttc CT-rich tract
taatactttcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG