Sequence
atgc intronic sequence ATGC exonic sequenceAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g22420.1 |
intron # | 25 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G168228_T01 (Zea mays), 5'ss of exon 4
AATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
||||||||| || |||||||| || |||||||||||||| || || ||||| ||| || |||||| | |||| |||||||| || |||||||||||||||||| | | | | ||||| | | | || || | || | ||| ||| || |||||| | ||| |||| || || ||||| |||
AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatactaccgatgctagaatt--------ttttatggtacttgtttttacaatcaaataatgattgttgt-taacctcttggctgtgattatttt-cag
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G370521_T01 (Zea mays), 5'ss of exon 3
AATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
||||||||| || |||||||| || |||||| ||||||| || || ||||| ||| || |||||| | |||| |||||||| || |||||||||||||||||| | | | | ||||| | | | || || | ||| | ||| ||| || |||||| | ||| || || || ||||| |||
AATTCTTAGTGTAATACTAGCCAAGGAAGATATGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatactaccgatgctagaatt--------ttttatggtacttatttttacaatcaaataatgattgttgt-taacctcttgaatgtgattatttt-cag
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 20
AATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
|||||||| || |||||||| || |||||||||||||| ||||| ||||| |||||| |||||| |||||| |||||||| || || ||||||||||||||| | | || | | | | | || || | | || | | | | ||| ||| ||| |||| | || || || | | | || ||||| |||
GATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGATGTTGATCTAGAAGCTATAGCTAACTTGACAGAAGGGTACTCGGGTAGTGATCTCAAGgta-tgatattac--tagcactaagaatt----tgttacggtacttagttttacaatcaaatattggttgtcg--ttaacctcttgac-tgattatttt-cag
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G482077_T01 (Zea mays), 5'ss of exon 3
AATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
||||||||| || |||||||| || |||||| ||||||| || || ||||| ||| || |||||| | |||| |||||||| || |||||||||||||||||| | | | | | ||| | | | || || | ||| | ||| ||| || |||||| | ||| || || || ||||| |||
AATTCTTAGTGTAATACTAGCCAAGGAAGATATGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatactaccgatgctcgaatt--------ttttatggtacttatttttacaatcaaataatgattgttgt-taacctcttgaatgtgattatttt-cagMapped 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|33680639|gb|CF308878.1|CF308878EST: TTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAG AATCTATGTATTACTGCTGCTCATCTCCCTATTAAAGATATCCTTGAAAAG
genomic: TTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgt ... catttttcagAATCTATGTATTACTGCTGCTCATCTCCCTATTAAAGATATCCTTGAAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG