Sequence
atgc intronic sequence ATGC exonic sequence...ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctgggatctggtgttgttagctattttatactaatggagatttctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04814.4 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 1
---ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctgggatctggtgttgttagctattttatactaatggagatttct-ttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
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cttgattcaaatctagaatttattgacctg-gtaaaaatttattttcaattttgaat--ggt-ttgtttgccagtatgaactaatgaagaatgctatcccttagGCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTATATGGCCCTCCTGGAACAGGAAAGTCTTACTTGGCAAAAGCCGTCGCAACCGAGGCTGATTCAACATT
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G088834_T03 (Zea mays), 3'ss of exon 1
ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctggg-atctg-gtgttgttagctattttat--actaatggagatttct-ttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
|| | || | |||| | | | ||||||||| |||| | | |||| ||||||| | ||| | || ||||||| ||| | | | | | ||| || ||||| || |||||||| |||||||||||||| || ||||||||||||||||||||||||||
----aattat-acaaaaaaacatcatatgtctgaactcattggaagtgtagatatcttcgtgttgtcaactagtacatgtactaatgaagaatgccatcccttagGCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA--------------------------------
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 1
ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctggg-atctg-gtgttgttagctattttat--actaatggagatttct-ttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAA-GCTGTTGCAACTGAGGCTGATTCTACATT
|| | || | |||| | | | ||||||||| |||| | | |||| ||||||| | ||| | || ||||||| ||| | | | | | ||| || ||||| || |||||||| |||||||||||||| || |||||||||||||||||||||||||| ||| ||||||||||| ||||||||||| || |
----aattat-acaaaaaaacatcatatgtctgaactcattggaagtgtagatatcttcgtgttgtcaactagtacatgtactaatgaagaatgccatcccttagGCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAAAAAGCTGTTGCAACCGAGGCTGATTCAACGT-
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 1
ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctgggatctggtgttgttagctattttatactaatggagatttctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
||||| || | | | | |||| | | | || | | || ||| ||||| || || || |||||| || || | | || ||||| |||||||| |||||||| || || ||||||||||| || ||||||||||| |||||||| ||||| ||||| ||||| ||
-gtaaatttgtgtaatctggagctattcat-tgaagt--tttgaaaccgttctctttgtaaagttgtgagctttat-ctgttgttttgttacttctta-gGAAAGAGACGGCCTTGGAGAGCTTTTCTGTTGTATGGGCCTCCTGGAACAGGAAAATCGTATTTGGCTAAGGCTGTTGCCACTGAAGCTGACTCTACCTT
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 1
ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagt-ctgggatctggtgttgttagctattttatactaatggagatttctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
|| | | | ||| || | | | | || | | |||| | | || | || | | || | | | ||| ||| || | ||||||||||||||||||| || ||||||||||||||||||||||| || || | || || ||||||||||| || || |||||||||||
-aagaaagaaaaaaaagaaatgattttaatgttgagaagtcgtggatgctggattttagtttgattctatctgttctcatgctcctcccactccccttcagGAAAGAGACGACCATGGAGGGCTTTTCTGTTATATGGTCCACCAGGAACAGGAAAATCATACCTAGCCAAGGCTGTTGCAACCGAAGCAGATTCTACATT
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 1
ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctgggatctggtgttgttagctattttatactaatggagatttctttcttaagGTAAACGGAGA-----CCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
|| | | || || | | || | || || ||| | | | | || | || | | | ||| |||| || ||| | | | ||| || |||||||||||||| |||||||||||||| |||||||||||||| || || || || ||||||||||| || || || || |||||
-gttg-cttcatctttatcatctgttaaacttaaa---atgctaaatggttattatttttccttttcgtgttcaacaatttgcttgatctcttactcaagtttagGGAAGAGACGGCCCTGGAGGGCTTTTCTATTGTATGGTCCACCTGGAACAGGAAAGTCATACTTAGCCAAGGCTGTTGCAACAGAAGCAGACTCAACATTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|300215967|gb|HO088593.1|HO088593EST: GCTGCAGGAGGCCGTCATATTGCCTGTCAAGTTCCCGCAGTTCTTTACGG GTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAG
genomic: GCTGCAGGAGGCCGTCATATTGCCTGTCAAGTTCCCGCAGTTCTTTACGGgtgagcggct ... ctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAG
EST:
gi|33381146|gb|CF196489.1|CF196489EST: GCTGCAGGAGGCCGTCATATTGCCTGTCAAGTTCCCGCAGTTCTTTACGG GTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAG
genomic: GCTGCAGGAGGCCGTCATATTGCCTGTCAAGTTCCCGCAGTTCTTTACGGgtgagcggct ... ctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctgggatctggtgttgttagctattttatactaatggagatttctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
tactaat putative branch site (score: 1)
tttctttctt putative PPT
tattttatactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtaaacaacgactataaaaaaatgtgtacatgaactcatcttaagtctgggatctggtgttgttagctattttatactaatggagatttctttcttaagGTAAACGGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT