Sequence
atgc intronic sequence ATGC exonic sequencegtacgacgatcttgcttaattttgatctgtgtaagaagaagaagatggctgatcgattgcagttgctgtggcggtgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g47016.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g47016.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G061101_T02 (Zea mays), 3'ss of exon 3
-------gtacgacgatcttgcttaattttg-atctgtgtaagaagaagaagatggctgatcgattgcagttgctgtg-gcgg-------tgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
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gtacgtagtaccatgacaacacatgcatatgcgtgcatgtaagatcatgcaatgcgacacttgacgacgcacgccgcgcgcggccatgcatgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTCGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGGCGC
upper sequence: LOC_Os03g47016.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G002225_T01 (Zea mays), 3'ss of exon 4
------------------gtacgacgatcttgc---ttaattttg-atctgtgtaagaagaagaagatggctgatcgattgcagttgctgt-ggcgg--------tgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
| ||| | ||| ||| || | ||| | | ||||||| | | | | | | | | | | ||| | ||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||||| | | |
gtacgcgagagtttccacgcacgtccatcatgcatgttcgtattgtagttttgtaagatcatgcaatgcaccacttggtgacgcacgacgccggccgcatgcgtatgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTCGAAGCGAAGCAGATCAACAATTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCAGGCAC
upper sequence: LOC_Os03g47016.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------------------------------------gtacgacgatcttgcttaattttgatctgtgtaagaagaagaagatggctgatcgattgcagttgctgtggcggtgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
|| | | | ||| | | || | | | | | ||| | |||| | | |||| || |||||| | ||| || || ||| | || || ||||||||| | |||||||||||||||||||| || |||||||| ||||| |||||||| ||| |
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttga-catttgct-tcgttgtgctgg-acagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG
upper sequence: LOC_Os03g47016.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
----------------------------------------------------------------gtacgacgatcttgcttaattttgatctgtgtaagaagaagaagatggctgatcgattgcagttgctgtggcggtgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
|| | | | ||| | | || | | | | | ||| | |||| | |||||| || |||||| | ||| || || ||| | || || || |||||| | |||||||||||||||||||| || |||||||| ||||| |||||||| || |
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttga-catttgct-tcgctgtgctgg-acagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgtgtaagaagaagaagatggctgatcgattgcagttgctgtggcggtgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
ggctgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgacgatcttgcttaattttgatctgtgtaagaagaagaagatggctgatcgattgcagttgctgtggcggtgcagGAGCTGGAGAAGGCGGCGCTGGCGGAGTCGACGGGGCTGGACGCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGCCACTGGAAGCCGACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG