Sequence
atgc intronic sequence ATGC exonic sequence...agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g10784.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
agttttttgaacaccatgttaccgtcccttcctcaaatatctatg--tatttgtgcaagtagacggtt--gtcaaattgtgcatatttg-gttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
||| ||| || | | | | | || ||| | || ||| || | || || |||| | || | | ||| | |||||||||||||||||||||||||||||||| || || |||||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||||||||||
-----tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
-agttttttgaacaccatgtt---accgtcccttcctcaaat-atctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG-
|| | | | | || | | ||| || |||| | || | | | | | | | | ||| | ||| | | || | | || | ||||| ||||||||||| ||||| || | |||||||||||||| ||||| |||||||| | ||||| || ||||| ||||| || |||||||||
tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggt--tcattggatta---aaattctgctttcatg-attagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttg---tgcaagtagacggttgtcaaattgt----gcatatttggttctcttttgta-agCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
|| ||| || || || || | ||||| | ||| | | ||||| || || | | | | | || | |||||||| |||||||||||||| ||| | || || ||||||||||||| ||||| || |||| || || || || ||||| ||||||||||||
------------------gtatgatccttttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G16340.3 (Arabidopsis thaliana), 3'ss of exon 10
----agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgta-agCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
|| || |||| ||| | || ||| || || ||| | | || | | | | | || ||| || || | |||||||| |||||||| ||||| ||| | || ||| ||||||||||||| ||||| || | || ||||| || || ||||| ||||||||||||
gtatggtcattagaacg--atgctctgagtaatttaagaaaatgcttggtgttt-taaagctaaatcagaattggtctaaactcaaacataccttgtttatatagTTAGATGGTGGGGGTGTTGCTAGTGGTGGCCTTCGCGAATTAATACCATGCATAGCAAGAACCGCCGTAGCTGTTGGTGTCGATGGAATTTTCATGGAG
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgta-agCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
|||||| ||| | | | | | | | || || | | | | || | | | ||| | |||| || || ||||||||||| ||||| || | || ||| | ||||||||||| || ||||| | |||||||| ||||| ||||| ||||||||||||
-taaatttgaatgccacataatattttagatgctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAGMapped 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|157651751|gb|EX451385.1|EX451385EST: GTAGCTGATGTAACGCATGCTCTACAACAGCCTGCTGGAAAAAAG CTTGATGGTGGAGGTGTTGCAAGTGGAGGCTTACGAGAACTAATACCATGC
genomic: GTAGCTGATGTAACGCATGCTCTACAACAGCCTGCTGGAAAAAAGgtatatttac ... cttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
tttggttctctttt CT-rich tract
ttttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA