Sequence
atgc intronic sequence ATGC exonic sequencegtagatagcatagcttacagaaaaacattggatgaacttccatgttcaactgcatatactttggttagcagGATGGGAGCTCTAGCAACACTGACACAGTTCCTACCCCGAAAGTTATAATAGATCAAGACTCAGATCCGGATGCGACCATTGTAGAGATAACTTTGGGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g14440.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g14440.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120579_T01 (Zea mays), 3'ss of exon 2
gtagatagcatagcttacagaaaaacattggatgaacttccatgttcaactgcatatactttggttagcagGATGGGAGCTCTAGCAACACTGACACAGTTCCTACCCCGAAAGTTATAATAGATCAAGACTCAGATCCGGATGCGACCATTGTAGAGATAACTTTGGGTG------
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gtacatagcataggttacctaaaa-cattgggtgaacttccttgttcaaccacgtatactttggttagcagGATGGGAG------CAACACTGATATAGTCCCTATCCCGAAAGTTATAATAGACCAAGACTCAGATCCGGATGCAACCATTGTAGAAATAACCTTGGGTGATCGTC
upper sequence: LOC_Os08g14440.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0018g01780.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------gtagat-agcatagcttacagaaaaacattggatgaacttccatgttcaactgc--atatactttggttagcagGATGGGAGCTCTAGCAACACTGACACAGTTCCTACCCCGAAAGTTATAATAGATCAAGACTCAGATCCGGATGCGACCATTGTAGAGATAACTTTGGGTG
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gtatcaaatgatgccaatttatgttatgggttgtcgttgagtgtcaaattcttcttatttctttttgtctttggttgttggactggtggaacagGATGGGAAACCAGATGGAAATTATGATGATACTGATGCAATTCCCACTCCCAAAGTTATAATAGATCAAGACTCGGATCCAAATGCAACTATTGTGGAGA------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagaaaaacattggatgaacttccatgttcaactgcatatactttggttagcagGATGGGAGCTCTAGCAACACTGACACAGTTCCTACCCCGAAAGTTATAATAGATCAAGACTCAGATCCGGATGCGACCATTGTAGAGATAACTTTGGGTG
agcttac putative branch site (score: 3)
atatacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatagcatagcttacagaaaaacattggatgaacttccatgttcaactgcatatactttggttagcagGATGGGAGCTCTAGCAACACTGACACAGTTCCTACCCCGAAAGTTATAATAGATCAAGACTCAGATCCGGATGCGACCATTGTAGAGATAACTTTGGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA