Sequence
atgc intronic sequence ATGC exonic sequencegtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g53720.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G463904_T01 (Zea mays), 3'ss of exon 23
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA
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----------------------------------------------------------------------------------------ttttcattcttatctcctgagt-tcagaat-tcaaatatgctgacaacttatgtgacttgtac----ggctgttaattaaataatattactaatgcactgtgacagATAACCTTGCTTCAGCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGA
upper sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 24
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA---------------
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-------------------------------------------------------------------------------------------------------------cctgagttcagaattcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactgtgacagataaccttgcttcagCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGAAAACTTGAGCGAAAA
upper sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGC-ACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------
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-------------------------------------------------------------------------------------------------------------tgccggatt-ttgta-gtgtttgatatat-tataatggtatcattctgcctattgaaacttaagttgacaagttactgactgcata-agctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
upper sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGC-ACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------
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--------------------------------------------------------------------------------------------------------------tttgtagtgtttcatttattataatggtattttatt-atcattctgcctatt--taaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
upper sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcat-ttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------
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-----------------------------------------------------------------------------------------------------------------------------------gtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttct-tgcttgaaa-------attgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
upper sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------
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--------------------------------------------------------------------------------------ttatatctgtatcccttaatatattttgaa-----aaatgtgtt-actattttcccttttgaaacttctctccatctactaactaatgtagtt---------tgctaaacaacagTTACATAC--TCAA---------CACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTAMapped 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|88730804|gb|CI754417.1|CI754417EST: CTGGCCACACTGGGCACAAGTTCCCAAAGATGTGTCTTTATGTAAACCAG ATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTC
genomic: CTGGCCACACTGGGCACAAGTTCCCAAAGATGTGTCTTTATGTAAACCAGgtgatgcatc ... cctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA
tgttaac putative branch site (score: 2)
ttattttcct putative PPT
agtgatattattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG