Sequence
atgc intronic sequence ATGC exonic sequencegtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgtgcagctagtaattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 7
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgtgcagctagtaattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
||||||||| | ||| | | || || ||||| |||| || | || | | || || || | |||||| || || || | ||||| ||| | ||||||||||||||| |||||||| || || || ||||| |||||||||||||| ||||| ||||| |||||||| || |||||||| ||||||||
--------------------------------------------------------tgttttttt---tctaaaaagcaagagtgctaa-tctattatgttca---aacaacttaccttata-tgacttctgttgtctaatatgcaa-cttgaattaatgaacagATATTGTGTATGCCGATGCGTCTCCACTAGTCACATCTGTCTTAGATGGCTACAATGTATGCATCTTTGCTTACGGACAGACGGGAACAGGAAAGACTTT
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgt-gcagctagtaattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
|| || | | | ||| || | || | || | || || || |||| ||| | || | | | | || |||| | | ||| |||||| | ||| |||||||| || |||| | || || |||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||
-------------------------------------------------gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgc---tttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G02620.1 (Glycine max), 3'ss of exon 10
gtatttctaac-tatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgtgcagctagtaattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
|||| | || | | | | ||||| | ||| |||| | || | | | ||| | || | | | | | ||| || | | ||||| | | | | | | | | | ||| | || || ||| |||||| | ||| |||||||| || |||| | || || |||||||||||||||| ||||| ||||| || || |||||||||||||||||||| ||
gtatctgaaaagtgtaacacaatagctatttg----cttgagccttgaatgtcatcgc----tcttatatat------ttagtacaagatttttattattta----tcataattggaacttttctaaacaacagtgttt--tctatg---ttttaa-------cagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGGCAAACAGGAACAGGGAAGACATT
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggta-gctctataatgtgca-gctag-taattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
| | ||| | | ||| || | ||| | ||||| | || ||||| ||| | | | ||||||| |||||| | |||||||| ||||| ||||| ||| ||| | || ||||||||||| || || ||||| |||||||||||||||||||| ||||| ||
----------------------------------------------------------------------------------gtagcgtgctatgtcatggtcaagttagatcattaagtttaaataaca--gtaacaattaacaaagtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ04247 (Selaginella moellendorffii), 3'ss of exon 8
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgtgcagctagtaattaaagcaatggtgcattataacat-ctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
| |||| || |||| || || | ||| || ||| ||||| | |||||||||| |||| ||| || | ||||| | ||| || ||| ||||||||||||| |||||||||||||| |||||||||||||| || || || || ||
-------------------------------------------------------------------------------------------------------gtgagta--tatggcaa-agtctatattcacaagctgatcctcg--tttccgtt---gtgcagCTGAAGTGTTTGCAGACACGTCTCCGGTCGTTGTATCTGTCCTGGATGGCTACAACGTGTGCATATTTGCCTACGGACAAACAGGTACTGGCAAAACATTMapped 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|87015549|gb|CI303155.1|CI303155EST: TAAGAAGACATTCAAGTTTGACAGAGTCTACATGCCGACAGACAATCAAG CTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCT
genomic: TAAGAAGACATTCAAGTTTGACAGAGTCTACATGCCGACAGACAATCAAGgtatttctaa ... taatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
attataacatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgtgcagctagtaattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA