Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtacaatctgttgaggtgtgataattagtacttggattatttgtttgctgagagtcctaactctgtttcaattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 13
gtaaagtacaatctgttgaggtgtgataattagtacttggattatttgttt-gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
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-----gtacagttatctgagtcaagcttgaacatgccta-ataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 13
-----gtaaagtacaatctgt-tgaggtgtgataattagtacttgg--attatttgttt--gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
||| ||| ||| | ||| | ||| | | ||| | |||| ||| || || || | |||||||||||| |||||||| |||||||||||||||| ||||||||||| | | ||||||||||||||| ||||||||| | ||||| || || || ||||| ||||||||||
gtacagtattatactatccgagtgaagcctgacgacca-tacctaataattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 8
-----gtaaagtacaatctgt-tgaggtgtgataattagtacttgg--attatttgttt--gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
|| ||| ||| | ||| | ||| | | ||| | |||| ||| || ||| || |||||||||||| |||||||| |||||||||||||||| ||||||||||| | | ||||||||||||||| ||||||||| | |||| || || || ||||| ||||||||||
gtacaatattatactatccgagtgaagcctgacgacca-tacctaataattaattgatttagctaggaagtgtaactctgtttctgattatacagagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGAGAGCTCATTGGTTGTCATGTCCAAAG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 9
-----gtaaagtacaatctgt-tgaggtgtgataattagtacttgg--attatttgttt--gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
||| ||| ||||| ||| | ||| | | ||| | |||| ||| || || || | |||||||||||| |||||||| |||||| ||||||||| ||||||||||| | | ||||||||| ||||| ||||||||| | ||||| || || || ||||| ||||||||||
gtacagtattatactatctgagtgaagcctgacgacca-tacctaataattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTAGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACGGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G508368_T01 (Zea mays), 3'ss of exon 6
-----gtaaagtacaatctgt-tgaggtgtgataattagtacttgg--attatttgttt-gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
||| ||| ||| | ||| | ||| | | ||| | | |||| || ||| || || | |||||||||||| |||||||| |||||||||||||||| ||||||||||| | | ||||||||||||||| ||||||||| | ||| | || || || ||||| ||||||||||
gtacagtattatactatccgagtgaagcctgacgacca-tacctagtaattaattatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACAGGAGCTCATTGGTTGTCATGTCCAAAG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 7
-----gtaaagtacaatctgt-tgaggtgtgataattagtacttgg--attatttgttt--gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
|| ||| ||| | ||| | ||| | | ||| | |||| ||| || || || | ||||||| |||| |||||||| ||||||| |||||||| ||||||||||| | | ||||||||||||||| ||||||||| | ||||| || || || ||||| ||||||||||
gtacaatattatactatccgagtgaagcctgacgacca-tacctaataattaattgatttagccaggaagcgtaactctatttctgattatacacagGACTGAATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 13
gtaaagtacaatctgttgaggtgtgataattagtacttggattatttgttt-gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG---------
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-----gtacagttatctgagtcaagcttgaacatgccta-ataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGGTCTGAATT
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 13
-----------------------gtaaagtacaatctgttgaggtgtga-taattagtacttggattatttgtttgctgag--agtcctaactctgtttcaattatacat---agGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
|| | | || ||| ||| | | || || | || |||| | ||| || || || | || || | | |||||||||| ||||| ||||||||||| |||| ||| || | |||||||||| ||| ||| |||||||| || ||||| ||||||||||
gtgggttttttcttccttgatttatataattca-tcttttgttaaataaatacgtatgagttaaattaaataattgatgtcttggtgctgggctgctggcattttgatctctcagGACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGMapped 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|218490208|gb|FG966190.1|FG966190EST: CTGGTTTCCTTTCTCAAGTTCATGAGCTCTCACCAGTTTTTCTGCATAAG GACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCT
genomic: CTGGTTTCCTTTCTCAAGTTCATGAGCTCTCACCAGTTTTTCTGCATAAGgtaaagtaca ... ttatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtacttggattatttgtttgctgagagtcctaactctgtttcaattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
tcctaac putative branch site (score: 1)
tttcaattatacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtacaatctgttgaggtgtgataattagtacttggattatttgtttgctgagagtcctaactctgtttcaattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT