Sequence
atgc intronic sequence ATGC exonic sequence...gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgattgtgagattgcaatgtaacctttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g56050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 4
gtgtatcttggtgagtacca-gtacacaagtacttgggatgaattgattagtttttggaaacaaagatttga---ttgtgagattgcaatgtaacctttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
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------gtaagtacgcgcttcgtatctaattactgcagtttatcaggtgtctctctaaacaagaggtctcaggttttgtctccttgtgttttctggttgtctagGCGGGTATGACGTGGAGGAGAAGGCCGCGAGGGCATATGACCTGGCGGCGCTCAAGTACTGGGGGACGTCCACGCACGTGAATTTCCCG
upper sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgatt-gtga-gattgcaatgtaacctttgct--agGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
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---ta-ctagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
upper sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgattgtgagattg-caatgtaacctttg--ctagGTGGG--TATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
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--gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactctt--gctactgtt-tataattgttacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
upper sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 6
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgat--tagtttttggaaacaaagatttgattgtgagattgcaatgtaacctttgcta------gGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
||| | | || | | || | | || | || |||| || | ||||||| | | | | | | |||| | ||||| ||||||||||| ||||| || || ||||| ||||||||||| || |||||||| ||||| ||||| |||||||| |||||| ||
-------gctacaagtccttttccaaagggtctgcattttcaatgctcatacttttacagaatactaatttgat-gaggggtgaattttttttgtttgtgaactgaagGTGGTTATGACATGGAAGAGAAAGCCGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACGCACATAAACTTCTCG
upper sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
------gtgtatcttggtgagtaccagtacacaagtact---tgggatgaattgattagtttttgg-aaacaaagatttgattgtgagattgcaatgtaacctttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
| | | | | || | | | | || | | | | || | || || || | | || || |||| |||| || ||||| ||||||||||| ||||| | || |||||||||||||| |||||||||||||| || || || |||| ||| ||| |
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
upper sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgattgtgagattgcaatg----taacc---tttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
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----------gtaagcccccttttctttttggtcgaaatgaagaaacca-tgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtttttggaaacaaagatttgattgtgagattgcaatgtaacctttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
atgtaac putative branch site (score: 3)
cctttgct CT-rich tract
aaagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgattgtgagattgcaatgtaacctttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - cttggtg
- - - - - - - - - - - - - - gtacttg
- - - - - - - - - - - - - - - - - - gatgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatg