Sequence
atgc intronic sequence ATGC exonic sequence...tgatgaactgatcgatgatcatcatgttctgaatttgttgattttgtggctggttgatcatcatcattcatcatcatcttgtttcttgtttcatctgcagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
Basic information
species | Oryza sativa |
transcript | LOC_Os08g06060.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G123886_T02 (Zea mays), 3'ss of exon 1
tgatgaactgatcgatgatcatcatgttctgaatttgttgattttgtggctggttgatcatcatcattcatcatcatcttgtttcttgttt-catctgcagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
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--gtgcgtacgtcgtcctccctcatc-----gatcgccttctcgtttgttcgttcgggcttcactactagtacgtaccggatcttttgtgcatgcatgcagTGCTGCTGTGAACGCGCAGACTCGCGAGGAGGTCGCCATCAAGAAGATCGGCAACGCGTTTGACAACCAGATCGACGCCAAGCGCACTCTCCGAGAAATC
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDO98258 (Chlamydomonas reinhardtii), 3'ss of exon 2
-------------------------------------------------------------------------------tgatgaactgatcgatgatcatcatgttctga------atttgttg-attttgtggctggttgatcatcat--cattcatcatcatcttgtttcttgt--ttcatctgcagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
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gtgagccagctgggggttggacggtcggcgggggcgtgtccttgctgctgcggctgctaccctcctggacccgttgttcttccgcaccaaaccttcatc-tcacgcacggacctgccaccccctgcattccataccgtccctacctccactacatccaaacacatcccactaccgacaactcccacacagCTCCGCCAAGAACCTGGACAACCAGGAGAAGGTGGCCATCAAGAAGATCGCAAACGCCTTTGACAACGTCATCGACGCCAAACGCACCCTGCGCGAGATC
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S59_325V6.1 (Physcomitrella patens), 3'ss of exon 1
tgatgaactgatcgatgatcatcatgttctgaa-tttgttg--attttgtggctggttgatc-atcatcattcatcatcatcttgtttcttgtttcatctg---cagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
| || | | | | | | |||| || ||||| | || |||||| | |||| | | ||| ||| || | ||| ||| | | ||||||| | | || | |||||||||| |||||||||||||| ||||||||||||||| ||| || || |||||||| |||||||| ||
-----atttgcccctttacc--cgtcttctcaactttgtcacagtcgtgaggctggaactcctgaaatcagttactgatttctgatttgctgatgattcttggctagTTCCGCTGTGAATTCTGAAACGGGAGAGGAGGTGGCCATCAAGAAGATCGGTAACGCGTTCGACAACAGGATTGATGCAAAGCGCACTCTGCGAGAAATT
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ22596 (Selaginella moellendorffii), 3'ss of exon 1
tgatgaactgatcgatgatcatcatgttctgaatttgttgattttgtggctggttgatcatcatcattcatcatcatcttgtttcttgtttcatctgcagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
||| || | | | | | | | | | | |||| || | ||| || | || | | | |||||| ||| | | ||||| |||| | || || || |||||||| |||||||| || ||||||||| |||||| ||||||||||| |||| ||||||
--gtgag-tgtgctccttcctccgtctcccaattggggtcgatttgccccttgcctgctctcaaagctcgccgtc---tcataccaagtttcacgcacagCTCTGCAGTGAACAGCGAGACCAACGAAGAAGTTGCTATCAAGAAAATCGGCAATGCCTTCGACAACAGGATCGATGCCAAGCGCACATTGCGCGAGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggctggttgatcatcatcattcatcatcatcttgtttcttgtttcatctgcagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
ggttgat putative branch site (score: 5)
tcttgtttcttgtttc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatgaactgatcgatgatcatcatgttctgaatttgttgattttgtggctggttgatcatcatcattcatcatcatcttgtttcttgtttcatctgcagTGCGGTTGTGAATGCGCAGACTCGTCAGGAGGTGGCAATCAAGAAGATCGGCAACGCGTTCGACAACCAGATCGACGCCAAGCGCACCCTGCGAGAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
tgatgaa
- - - - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - ttgttga
- - - - - - - - - - - - - - - - - - - - - - -gtggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcat