Sequence
atgc intronic sequence ATGC exonic sequence...cgcaactatttgcgccgaaatcactttgcagagtatacatacatgatcagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16600.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 1
cgcaactatttgcgccgaaatcactttgcaga-gtatacataca--tgatcagtcaatttggtaactgaccaaacttttttttttgttttgaattgtt----tgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
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------taatc-tgttgatgtcacgtgattgaagtatctattccactgatttgcttgtctgacgtcttgatggtctgtacaactgacattccaatgttcttttgcagGGATATGTGGTCCTAAATAGGCCGTGGGCATTTGTGCAGTGGCTTCAGAAAGCAAAGATTGAAGAAGA
upper sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G08020.1 (Glycine max), 3'ss of exon 1
cgcaactatttgcgccgaaatcactttgcagagtatacatacatgat------cagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
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-gaaaagtttatcatcaatttcattatttgttatatttctttattattccttgctgatgaattgacgtcttaaaaaaatttctttttttattt---ttggt--cagGGTTATGTTGTCATGAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGACATTGAGGAAGA
upper sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G03930.1 (Glycine max), 3'ss of exon 1
-cgcaactatttgcgccgaaatcactttgcagagtatacatacatgat--cagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
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tatcaactctat-catgaatgtcgttgtttgtgatctttctatattattcccatcaattcattctgtcatcaaaatttatgt--caatttatttttggtgcagGGTTATGTTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
upper sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
----cgcaactatttgcgccgaaatcactttgcagagtatacatacatgatcagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
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ctatcatgaatgtcattgtttgtgat-ctttctatattattccca-atttcccatcaactaacgctgtcatcaaaatttatatcct--cttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
aactgac putative branch site (score: 2)
aaacttttttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgcaactatttgcgccgaaatcactttgcagagtatacatacatgatcagtcaatttggtaactgaccaaacttttttttttgttttgaattgtttgcagGGCTATGTCGTACTAAATAGGCCCTGGGCATTTGTACAGTGGCTGGAGAAAGCAAAGATTGAAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - tgcgccg
- - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - atacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaccaaa