Sequence
atgc intronic sequence ATGC exonic sequenceGTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38150.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G375504_T03 (Zea mays), 5'ss of exon 11
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctatattttcaaagcgttgatactaccaatttgg---------ctaaacccgtaatacactgtgcag
|||||||||| || |||||| || || ||| |||||||||||||||||||||||| ||||||||| ||||| ||||| |||||||| || | ||||| | ||| |||| |||||||| || |||||| | ||||| | | |||
GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTTGTTACAAGTAGAGATGAAATCGCTGATTTACTAAAGgtaagtgtaa-----tatatcatgaaaataatgattctaccaatatgcatgataagcctaaactcataatatgttctacag
upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G094309_T01 (Zea mays), 5'ss of exon 4
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctat----attttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcag
|||||||||| ||| |||||| | || || |||||||||||||||||||||||||||| |||||| || || || ||||| ||||||||| | | || ||| || | | | || | ||| | |||||| | ||||||||| | |||
GTTATAACTGGTGCCATTCCTAGCAACGTGGGTGAAAAACTTATTGGCCTTGTTACAAGTAGAGACGAAATTGCTGATTTACTAAAGgtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacag
upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G552586_T01 (Zea mays), 5'ss of exon 4
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactg--tgcag-------------------------------------
|||||||||| ||| |||||| | || || |||||||||||||||||||||||||||| |||||| || || || ||||| ||||||||| | | |||||| | ||| | |||| ||||| | || | || | ||| ||| | ||
GTTATAACTGGTGCCATTCCTAGCAACGTGGGTGAAAAACTTATTGGCCTTGTTACAAGTAGAGAAGAAATTGCTGATTTACTAAAGgtgagcgtaa-----tatattatgaaaatgatgattgtaccattatgtcgtaagtctagataaacttatttcatattcagatataacataatttgcctttgttttctgcag
upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G389416_T02 (Zea mays), 5'ss of exon 2
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactg--tgcag-------------------------------------
|||||||||| ||| |||||| | || || |||||||||||||||||||||||||||| |||||| || || || ||||| ||||||||| | | |||||| | ||| | |||| ||||| | || | || | ||| ||| | ||
GTTATAACTGGTGCCATTCCTAGCAACGTGGGTGAAAAACTTATTGGCCTTGTTACAAGTAGAGACGAAATTGCTGATTTACTAAAGgtgagcgtaa-----tatattatgaaaatgatgattgtaccattatgccgtaagtctagataaacttatttcatattcagatataacataatttgcctttgttttctgcag
upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G472614_T01 (Zea mays), 5'ss of exon 6
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacc-cgtaatacactgtgcag------------------------------------------------
|||||||||| ||| |||||| | || || |||||||||||||||||| ||||||||| |||||| || || || ||||| ||||||||| | | |||||| | ||| | |||| ||||| | || |||| ||||| | | ||
GTTATAACTGGTGCCATTCCTAGCAACGTGGGTGAAAAACTTATTGGCTTTGTTACAAGTAGAGACGAAATTGCTGATTTACTAAAGgtgagcgtaa-----tatattatgaaaatgatgattgtaccattatgcctaattaatttaatata-taactagtctatcaagatgtttattccttgtaatccaccttctctttttttatag
upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 5'ss of exon 12
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtat-gcaattctatattttcaaagcgttgatactaccaatttggcta--aacccgtaata-cactgtgcag-
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GTTATCACTGAAGCTATCCCAGATACTGTTGGTGAAAAACTTATTGGACTTGTCACTACAAGAGAGCAGATTCCCGATTTGCTAAAGgtggggattgagattggatatgtttgatg-gtttttcataataggttggttattaacttgttttagttctgccccagMapped 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|88839043|gb|CI377967.1|CI377967EST: AACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAG CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTC
genomic: AACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgc ... cactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT