Sequence
atgc intronic sequence ATGC exonic sequencegtaaggtttttctttttctttcttcgatttcagtagagcagatgaagagcaatgtttattgagtagtgggtgattctgaactaagttctctcctttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43790.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43790.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 2
gtaaggtttttctttttctttcttcgatttcagtagagcagatgaagagcaatgtttattgagtagtgggtgattctgaactaag-ttctctcctttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG
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gtaaggttt--------cctcgtgcaatttcagtagag--aattgggcatggtgcttagatgctaataggtgtttctgagcgaaggttttcctctttcagTGATTGTAGGTGAGATTGCCAATTTCGTGGCATATGCTTTCGCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG
upper sequence: LOC_Os05g43790.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 2
gtaaggtttttctttttctttcttcgatttcagtagagca-gatgaagagcaatgtttattgagtagtgggtgattctgaactaagttctctcct-ttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG---------
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gttgaaggttaattaaaatatgcg-aattttagtttatcatggtcattttttctttatctgatttcttgcagaattcttttctgtatggtttattgttcagTGATTGTAGGAGAGGTTGCAAACTTCGTTGCATATGCATTTGCTCCAGCAGTCCTAGTTACTCCTCTTGGTGCATTAAGTATTATTGTGAGGTATTCCCC
upper sequence: LOC_Os05g43790.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G44980.1 (Glycine max), 3'ss of exon 2
gtaaggtttttctttttctttcttcgatttcagtagagca-gatgaagagcaatgtttattgagtagtgggtgattctgaactaagttctctcct-ttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG
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gttgaaggttaattaaaatatgcg-aattttagtttatcatggtcattttttctttatctgatttcttgcagaattcttttctgtatggtttattgttcagTGATTGTAGGAGAGGTTGCAAACTTCGTTGCATATGCATTTGCTCCAGCAGTCCTAGTTACTCCTCTTGGTGCATTAAGTATTATTGTGAG
upper sequence: LOC_Os05g43790.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0009g03650.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtaaggtttttctttttctttcttcgatttcagtagagcagatgaagagcaatgtttattgagtagtgggtgattctgaactaagttctctcctttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG
|| | | | | | | || || || || ||| ||||| || || || | | || | | ||| | | ||||||||||||||| ||||| ||||| || ||||| || ||||| || || ||||||||||| |||||||| ||| | || || ||||| ||
actcttaaccagtgtgaggacacatgattcaccatggactttcgttcttcac-tgac------tgtttgcagaatatctcttg--ttgtatgtatgatttctgatgt-agTGATTGTGGGAGAGGTTGCTAATTTTGTGGCATATGCATTCGCCCCAGCTGTTCTTGTTACCCCTCTTGGGGCATTAAGTATCATTGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagcaatgtttattgagtagtgggtgattctgaactaagttctctcctttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG
ttctctcctttc CT-rich tract
aatgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggtttttctttttctttcttcgatttcagtagagcagatgaagagcaatgtttattgagtagtgggtgattctgaactaagttctctcctttcagTGATTGTGGGAGAAGTTGCCAATTTCGTCGCATACGCCTTCGCTCCCGCGGTTCTTGTTACTCCTCTTGGAGCACTGAGCATAATTGTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA