Sequence
atgc intronic sequence ATGC exonic sequence...tatccatcagtaatctacctgggccctagttttagtaaacattgtgtaattgatggatttctatttcccagtgcttatgttgtcgtaattcattttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g25980.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 1
tatccatcagtaatctacctgggccctagttttagtaa-acattgtgtaattgatggatttctatttcccagtgcttatgttgtcgtaat----tcattttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
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----tattgaaagttgacttagagtaaagctaaaataagataatttggaattattactctgtttctccttggaaggtac-ttgccctaacatcctgtttccatagCTAGTGAAGCTTCTGAAGTCATGTGACTATCGAACTTTGGCAATCGGTGATGGTGGGAATGATGTAAGGATGATACAACAGGCTGACATTGGTGTAGGAA
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 19
-tatccatcagtaatctacctgggccctagttttagtaaacattgtgtaattgatggatttctatttcccagtgcttatgttgtcgtaattcattt--tgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
| | | | | || || || |||| | | | | ||||| || || | | || | ||| || | || || |||||||| || | ||||||||||||| ||| |||| ||||||||||| ||||||||||||||||| ||||||||||| || |||||||||||||| || |
ttctgtaacgggaacataatattgct---gtttgtattattctgctctaatttatcagaaaataatagcactgatttgtcctgtatacctttacttattgcagCTTGTACAGATCTTAAAATCATGTGATTATAGAACATTGGCTATTGGTGATGGTGGGAATGATGTAAGGATGATACAGCAAGCTGATATTGGTGTGGGCA
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 19
tatccatcagtaatctacctgggccctagttttagtaaacattgtgtaattgatggatttctatttcccagtgcttatgttgtcgtaattcattt--tgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
||| | | | | | || || || || || | ||||| || || | | || | |||| || | || || |||||||| || | ||||||||||||| ||| |||| ||||||||||| ||||||||||||||||| |||||||||||||| |||||||||||||| || |
--tccctaactggaacatattactgctgtttgtattatttcttctctaatttatcagaaaataatagcactgatttgtcttgtatacctttacttgttgcagCTTGTACAGATCTTAAAATCATGTGATTATAGAACATTGGCTATTGGTGATGGTGGGAATGATGTAAGGATGATACAACAAGCTGATATTGGTGTGGGCA
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 19
lower sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 18
------tatccatcagtaatctacctgggccctagttttagtaaacattgtgtaattgatggatttctatttc--ccagtgcttatgttg---tcgtaattc-attttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
| ||| | || | | | | ||| | | || | || | || || |||| | | || | ||| || | || | | ||||||| || || |||||||| | || ||||| || |||||||||||||| || |||||||| || ||||||||||| || || |
gtaccccacccaactttaggtgctataagtattcgattttcctagtaccaagtggccttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCAMapped 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|163929268|gb|EG711029.1|EG711029EST: TTTCAAAAACAGCAATATGCTGCCGGGTTACACCGTCTCAGAAAGCACAG CTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGAT
genomic: TTTCAAAAACAGCAATATGCTGCCGGGTTACACCGTCTCAGAAAGCACAGgtaaattcag ... cattttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaattgatggatttctatttcccagtgcttatgttgtcgtaattcattttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
aattgat putative branch site (score: 4)
ttcatttt putative PPT
taattcattttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatccatcagtaatctacctgggccctagttttagtaaacattgtgtaattgatggatttctatttcccagtgcttatgttgtcgtaattcattttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT