Sequence
atgc intronic sequence ATGC exonic sequencegtgagttacttcatttgcttttcttctttgctggtattattagaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g26914.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 3
gtgagttacttcatttgcttttcttctttgctggtattatt-----agaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
||||| || ||| |||| ||||| ||||||| ||||| | || ||| | |||| || |||| | || |||| | ||||||||||||| ||||||||| |||||||||||||||||||||||||||||||| |
gtgagcta-ttcttttgtctttctgctttgcttaatttattgcttcaaaatatcttccattctgatttg-attttaaatcttaaatgacagGATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG
upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 3
gtgagttacttcatttgcttttcttctttgctggtattatt-----agaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
||||| || ||| |||| || || |||||| |||||| | || || | || || ||||||| | || | || | ||||||||||||| | ||||||||| |||||||||||||||||||||||||||||||| |
gtgagcta-ttcttttgtcttcctgttttgcttacattattgcttcaaaatgtcttccgttcttacttggatttaa-atatcaaatgacagGATTTCTATAACGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG
upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtgagttacttcatttgcttttctt----ctttgctggtattattagaa------aatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
| | | ||||| || || || || | || ||| ||| | ||| |||| || || || | | || | ||||||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| |
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactga-atatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G14290.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtgagttacttcatttgcttttctt----ctttgctggtattattagaaa-atccagtttcctgacatggat----ttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
| | | ||||| || || || || | || ||| || || | | | || || || || | | || | ||||||| ||||| ||||| ||||||||||||||||||||||||||||| |||||||
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtgagcatgtgttttaaatatgtgattgtactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattactctgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGTGMapped 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|58608089|gb|CK036122.1|CK036122EST: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGGAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST:
gi|58660788|gb|CK049468.1|CK049468EST: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtattattagaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
atggatttgatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttacttcatttgcttttcttctttgctggtattattagaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA