Sequence
atgc intronic sequence ATGC exonic sequencegtatagccttgtgtactttttctgcagttctttggaaaattgatatctagaacccttcttttggatttactgctgtttgttgtatcagATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g36840.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 5
gtatagccttgtgtactttttct-gcagttctttggaaaattgatatctagaaccctt--cttttggatttactgctgtttgttgtatcagATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
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gtatggtcttgggtatccttccttgtagtttcttgtgaatcagttgtcttgagcccctgaccgttgaattta-tattgtttcttggatcagATGGCAATGGTTTCAAGACTAGTACGATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
upper sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G19100.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------------------------gtatagccttgtgtactttttctgcagttct--ttggaaaattgatatctagaacccttcttttggatttactgctgtttgttgtatc-agATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
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gtatgaatctttcgcttcattctctaaactctttatctttagttatgattctgcaacacatatctctgattctcattttgcattacataccattagttatgattttgaaactcagatctttaattatgattctgcatctcaccttcattattatctttagATGGAAATGGTTTCAAGACCAGCACAATGAGACTTGGGGCAGATGTCATCGTCTTCAGCCGCCATTCGAAGAACCA
upper sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g08750.t01 (Vitis vinifera), 3'ss of exon 5
gtatagccttgtgtactttttctgcagttctttggaaaattgatatctagaacccttcttttggatttactgctgtttgttgtatcagATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
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----------gtaaggatgttatgtttttcattctgcattttttttct----ccttccatatgagttggctgatgtgtagcattacagATGGAAATGGCTTCAAGACCAGCTCTATGAGACTTGGAGCAGATGTTATTGTCTTCAGCCGCCACCTGGACAATGG
upper sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g00870.t01 (Vitis vinifera), 3'ss of exon 6
gtatagccttgtgtactttttctgcagttctttggaaaattgatatctagaacccttcttttggatttactgctgtttgttgtatcagATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
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gtatggattc-cacctctcttctaccattt------acatttttcctcatcatcttgtact--aagtggttggcttctatcctttcagATGGAAATGGGTTCAAGACAAGCACAATGAGACTTGGAGCGGATGTGATTGTATTCAGCCGCCACTTGAAAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaaaattgatatctagaacccttcttttggatttactgctgtttgttgtatcagATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
aattgat putative branch site (score: 4)
attgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagccttgtgtactttttctgcagttctttggaaaattgatatctagaacccttcttttggatttactgctgtttgttgtatcagATGGAAATGGATTCAAAACTAGCACAATGAGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG