Sequence
atgc intronic sequence ATGC exonic sequencegtactcattacccaaatctttatacatttcactctattgtttccaattagaataaatgttgaccaaaatatcctatctgcatctagattagttttatcgtcaagagtcagtactaaaatatctttcaaaatacagGTTTGCAAATTTTTGGAGGTATCATGTTTGTCATTTTTACCGGAATATGGGCCTAAGCTAAAGGAAGATTATGTATCTGTTGGACACTTGCCAAAAATTC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g29050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 3
gtactcattacccaaatctttatacatttcactctat---tgtttccaattaga-at--aaatgttgaccaaaatatcctatctgcatctagattagttttatcgtcaagagtcagtactaaaatatctttcaaaatacagGTTTGCAAATTTTTGGAGGTATCATGTTTGTCATTTTTACCGGAATATGGGCCTAAGCTAAAGGAAGATTATGTATCTGTTGGACACTTGCCAAAAATTC
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-------gtactaaaagctttgtacatttcaaagtagacaccctcataattgaacattaaaatgttaatcagaacaccttatttg-------gctatctttat---------tcaat---------ttatttgcactacagGTTTGCAAATTTTTGGAGGTGTCATGTTTGTCATTTTTACCTGAGTATGGTCCCAAGTTAAAAGAAGACAATGTTTCAGTTGGACATTTACCAAAGATTC
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 4
gtactcattacccaaatctttatacatttcactctattgtttccaattagaataaatgttgaccaaaatatcctatctgcatctagattagttttatcgtcaagagtcagtactaaaatatctttcaaaatacagGTTTGCAAATTTTTGGAGGTATCATGTTTGTCATTTTTACCGGAATATGGGCCTAAGCTAAAGGAAGATTATGTATCTGTTGGACACTTGCCAAAAATTC
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----------------------------atgtttgatcttctcca-tttgatttctagttga---aactgtggtttttttattt---tatggtcactaaacgcttgtttttactataagaaattttatgttctagGTTTGCAAGTTTTTGGAGGTATCAAAGTTATCTTTTTCACCTGAATATGGTCCTAAGCTGAAGGAAGAATATGTGATGGTGAAGCATCTACCCAAAATCC
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 4
gtactcattacccaaatctttatacatttcactctattgtttccaattagaataaatgttgaccaaaatatcctatctgcatctagattagttttatcgtcaagagtcagtactaaaatatctttcaaaatacagGTTTGCAAATTTTTGGAGGTATCATGTTTGTCATTTTTACCGGAATATGGGCCTAAGCTAAAGGAAGATTATGTATCTGTTGGACACTTGCCAAAAATTC
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---------------------------------caaataaatgaaacaggtggcaccatgcac--gagtggtgtgcttgagagtggcaccactgcatagtacctggttcttacagtgggttattctatgctgtagGTTTGCAAATTTTTGGAGGTTTCGAAGTTATCATTTTCTCCGGAATATGGCCCAAAGCTGAAAGAAGATTATGTGATGGTCAAGCATTTACCAAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctagattagttttatcgtcaagagtcagtactaaaatatctttcaaaatacagGTTTGCAAATTTTTGGAGGTATCATGTTTGTCATTTTTACCGGAATATGGGCCTAAGCTAAAGGAAGATTATGTATCTGTTGGACACTTGCCAAAAATTC
tactaaa putative branch site (score: 1)
tatctttc CT-rich tract
tactaaaatatctttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcattacccaaatctttatacatttcactctattgtttccaattagaataaatgttgaccaaaatatcctatctgcatctagattagttttatcgtcaagagtcagtactaaaatatctttcaaaatacagGTTTGCAAATTTTTGGAGGTATCATGTTTGTCATTTTTACCGGAATATGGGCCTAAGCTAAAGGAAGATTATGTATCTGTTGGACACTTGCCAAAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA