Sequence
atgc intronic sequence ATGC exonic sequencegtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51630.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 1
-----gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtg-ggtttcgctgttc------gctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
||||| | || ||||| ||||||| || | ||| || | ||| ||| | | | | ||| ||||| || || | | | | ||||| |||||||||||| ||||||| |||||||||||| || ||||||||| ||||||| |||||| |||||| |||| || ||||||||| || | |
gtaaggtaagcgaccg-cgccgcactccattgctgcttt-ctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG
upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 1
gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtc-ccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
||||| || ||||| |||||||||||||| | | | ||||| | | | || | || | | || |||| |||| || ||||||| |||||| |||| | ||||||| |||||||||||| |||||||||||| ||||||| ||||| |||||| ||| || |||||||||||| | |
gtaagccagcg-cgccgcacgccattgccgccctcgttgtttac-ttcgcgtttggatctgtggctgaggagctgcgcgttggttggcctgtg-gccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAGCGGAAGCGCGAGGAACAGTGGGCCACCGAGAAGAAGGAGAAGGCCCTAG
upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 1
gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
||||| || ||| | | |||||||||||| | | | ||||| | | | || | | ||| | || || | || ||||||| ||||||||||| | ||||||| |||||||||||| |||||||||||| ||||||| ||||| |||||| ||| || ||||||||||| | |
gtaagccagcg-cgctgcacgacattgccgccctcgttgtttac-ttcgcgtttggatctgtggctgaggagctgtgggttggttggcctgtggccatgcagATGTCGTCCGAGGCGTCGAAGGTGGCGGTGCCGGAGTCGGTGCTCCGCAAGCGGAAGCGCGAGGAACAGTGGGCCACCGAGAAGAAGGAGAAGGCTCTGG
upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 1
gtaag---agctcgt-cgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtc-ccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
||||| ||| | ||||| |||||||||||||| | | | ||||| | | | || | || | | || |||| |||| || ||||||| |||||| |||| | ||||||| |||||||||||| |||||||||||| ||||||| ||||| |||||| ||| || |||||||||||| | |
gtaaggtaagccagcgcgccgcacgccattgccgccctcgttgtttac-ttcgcgtttggatctgtggctgaggagctgcgcgttggttggcctgtg-gccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAGCGGAAGCGCGAGGAACAGTGGGCCACCGAGAAGAAGGAGAAGGCCCTAG
upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G868433_T04 (Zea mays), 3'ss of exon 1
gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtg-ggtttcgctgttc------gctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
||||| | || ||||| ||||||| || | ||| || | ||| ||| | | | | ||| ||||| || || | | | | ||||| |||||||||||| ||||||| |||||||||||| || ||||||||| ||||||| |||||| |||||| |||| || ||||||||| || | |
gtaagcgaccg-cgccgcactccattgctgcttt-ctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGGMapped 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|218497125|gb|FG954384.1|FG954384EST: GCCTCCCCACTCCCCGTCTCCTCCTCCCTCACGCAGCTCGTCGAG ATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAG
genomic: GCCTCCCCACTCCCCGTCTCCTCCTCCCTCACGCAGCTCGTCGAGgtaagagctc ... cgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAG
EST:
gi|29641908|gb|CB646915.1|CB646915EST: CCCGCCTCCCCACTCCTTGTCTCCTCCTCCCTCACGCAGCTCGTCGAG ATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAG
genomic: CCCGCCTCCCCACTCCCCGTCTCCTCCTCCCTCACGCAGCTCGTCGAGgtaagagctc ... cgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctcgtcgccccgtcccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
atctgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA