Sequence
atgc intronic sequence ATGC exonic sequenceGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt...
Basic information
species | Oryza sativa |
transcript | LOC_Os07g46450.2 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G340359_T01 (Zea mays), 5'ss of exon 17
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagta-acagtttcaatcaactt----
|||||| | ||||||||| |||| |||||||| ||||||||||||||||||||||||||||||||| |||||||||| || ||||||||| |||||| || | ||||| || | | || |||| |||||||||| || || |||| ||| || || | | | ||
GCTAGAAGTAATGCAATCCTACAGGCAAGTTTAGAAAGAAGAAAACAAGCACTACATGAGCGCCGTGTGGCTCTGGAACAAAATgtatgct-tattctactagcttatgat----ttgtctgcttttatgcatccaaaatatatcagaagttcagccatttgttgtgtgcatacttgttatattttgtt
upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G036872_T02 (Zea mays), 5'ss of exon 17
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacag---tttcaatcaactt--
|||||||| ||||||||| |||| |||||||||||||||||||||||||||||||| ||||| ||| |||||||||| |||||||||||| |||||| || | || | || | | || |||| |||||| | | | || ||| || | || | | | ||
GCTAGAGGCAATGCAATCCTACAGGCAAGTTTGGAAAGAAGAAAACAAGCACTACACGAGCGTCGTGTGGCTCTGGAACAGGATgtatgccttattctactagcatacaa-----ttttctgcttttatgcatccaaaccccatttgttttgtgcatatttgttgtgaaagggcctctagctgagttgg
upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 5'ss of exon 17
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatg-----ctatattcttttaccc-tatgaattagtt--atttcattccatgcttccaa-----aatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt------------------------------------
|| | |||||||||||| |||||||| ||||||||||||||||| ||||| |||||||| || || |||| || || || |||||||| | || || | |||| | | | |||||| || | | | | | | || | ||| | | || | | | | |
GCAAAAGGAAATGCAATTTTACAAGCTAGTTTGGAAAGAAGAAAGCAAGCTCTACATGACCGTCGGCTGGCCCTTGAACAAGATgtatgtgtatccatcccggttcatttgcatgagggaaatgcacttcattggatatcccaagcggttattttagtataagtgtcatcgcat-tatccctcctctgagtaggccatatgcctgtcatttggggatgtttctgtacgttcag
upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 5'ss of exon 16
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgc-tatat-tcttttaccctatgaattag-----ttatttcattccatgcttccaaaatatgctgaaa-----atttcaccatctgtagtaacagtttcaatcaactt----------------------------------------------
|| | ||| |||||||| |||||||| || |||||||||||||| ||||| ||||||| || ||| |||| || || || |||||| || ||| || | ||||| ||| || | |||| || || ||| | ||| | ||| | || | || | || | |||
GCGAAAGGGAATGCAATTTTACAAGCTAGCTTGGAAAGAAGAAAGCAAGCTTTACATGACCGTCGTCTGGCCCTTGAACAAGATgtaagcgtatccatcctagaccctttgaccaaggaaaatgattttctttgtgtatttcaagacttgcaagattagttattgtaatgcaggttgccacgttgtccttgcccttattcaggtttttacaattattttattttattttattttttgttcag
upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ24423 (Selaginella moellendorffii), 5'ss of exon 16
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt
|||| |||||||||||| | ||||| |||||||||||| |||| |||||||| ||||| ||||| | ||||| || || || ||||||| | || || ||| | || |||| ||| || | |||| || ||| ||
GCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCATGATCGCCGGCTCGCTCTTGAACAAGACgtatgct-cgtgctattttcctttcc-ttttttatgagattt--tgacttcaaa-----ttgtaaacaccag----------------------------
upper sequence: LOC_Os07g46450.3 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ23838 (Selaginella moellendorffii), 5'ss of exon 16
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt
|||| |||||||||||| | ||||| |||||||||||| |||| |||||||| || || ||||| | ||||| || ||||| ||||||| | || || ||| | || |||| ||| || | |||| || ||| ||
GCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCACGATCGCCGGCTCGCTCTTGAACAGGACgtatgct-cgtgctattttcctttcc-ttttttatgagattt--tgacttcaaa-----ttgtaaacaccag----------------------------Mapped 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|25800836|gb|CA756797.1|CA756797EST: AACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT GTTTCAAGGTTGCAAGAGCAGCTACAAGCTGAAAGAGATCTTAGAGCTGCA
genomic: AACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctata ... gtacctctagGTTTCAAGGTTGCAAGAGCAGCTACAAGCTGAAAGAGATCTTAGAGCTGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGATgtatgctatattcttttaccctatgaattagttatttcattccatgcttccaaaatatgctgaaaatttcaccatctgtagtaacagtttcaatcaactt
- - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG