Sequence
atgc intronic sequence ATGC exonic sequence...atattttcaaagctgtaagttggaaagcttatggaactcaccatttttgtgctactttctataaattcttacctttgatgtaaatggttttgatcatcagGCTGTTGCTGCTGCAAGGATGAAGGGGGAATATCCTCAAAGAATTGGTCAACCTGAATGTCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g28270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 2
-atattttcaaagctgtaagttggaaa--gcttatggaactcaccatttttgtgctactttctataaattcttacctttgatgtaaatggttttgatcatcagGCTGTTGCTGCTGCAAGGATGAAGGGGGAATATCCTCAAAGAATTGGTCAACCTGAATGTCAA
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taatttatcactctcttttgttggaacatgcttatttgtcctgctgctcataaatt-ctacccaaacatg-tgaataatgattttagtggtct-gactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAGCCTGAATGTCAA
upper sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G146514_T03 (Zea mays), 3'ss of exon 2
-atattttcaaagctgtaagttggaaagcttatggaactcaccatttttgtgctactttctataaattcttacctttgatgtaaatggttttgatcatcagGCTGTTGCTGCTGCAAGGATGAAGGGGGAATATCCTCAAAGAATTGGTCAACCTGAATGTCAA
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aattatcgctctttcttttattggaacatgcttctttgttgtactgctcataatttctacccgaacttgtgaataatgattttagtggtct-gactgttagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGGCAGCCTGAATGTCAA
upper sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 1
---------------------atattttcaaagctgtaagttgg------aaagcttatggaactcaccatttttgtgctactttctataaattcttacctttgatgtaaatggttttgatcatcagGCTGTTGCTGCTGCAAGGATGAAGGGGGAATATCCTCAAAGAATTGGTCAACCTGAATGTCAA
| || | ||||| ||| |||| || | | | | | | |||| | | || | || | | | | | | || ||| | | || |||||||||| || || ||||| ||| ||||||||||||| ||||||||| |
gtactgactctgtttctgtgtttgttctttcctctgtatcttgttgactcaaagtttgtagctttgagggtctgtgtgtgtgtgtgattacaagctgatgaatagtct---cgtatccaatttctagGTTATAGCAACTGCAAGGATTAAAGGAGAATACCCTGAAAGAATTGGTCAGCCTGAATGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtgctactttctataaattcttacctttgatgtaaatggttttgatcatcagGCTGTTGCTGCTGCAAGGATGAAGGGGGAATATCCTCAAAGAATTGGTCAACCTGAATGTCAA
tttctataaattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattttcaaagctgtaagttggaaagcttatggaactcaccatttttgtgctactttctataaattcttacctttgatgtaaatggttttgatcatcagGCTGTTGCTGCTGCAAGGATGAAGGGGGAATATCCTCAAAGAATTGGTCAACCTGAATGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - agctgta
- - - - - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - -tgctact