Sequence
atgc intronic sequence ATGC exonic sequencegttactatgtctcactttgttaacttgtgtttccgcccattgtccttttgctaccatttctaaactctgctatttattgtttatttgcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g34210.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G091560_T01 (Zea mays), 3'ss of exon 3
gttactatgtctcactttgttaacttgtgtttccgcccattgtccttttgctaccatttctaaactctgctatttattgtttatttgcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
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gttgttgtccccaactct---aacctttttttgc------tggcttttttctaccaagtactaatt-----att--ttctctatctacatcatcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCCGACTATAGATATTTTCCAGAACCTGATCTTCCTGAAGTAGTTATCACTAGTGACTATATTAATG
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G34500.1 (Glycine max), 3'ss of exon 3
----gttactatgtctcactttgttaacttgtgtttccgccc----attgtcctt--ttgctaccatttctaaactctgctatttattgtttatttgcatcct---cagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
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gtgtaatcttgtacttttctttctagtctagtgtagcaagtacaagattgtttttcatttttatttcttcagacttgtattcttaaataacttctgttattctgtttagAGAACAATTACAATGAGGAAAAAGGAAGGGCTTGCTGATTATCGATATTTTCCAGAACCAGACCTTCCAGCAGTAATCCTTTCTCAAGAATATGTTGATG
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G05190.2 (Glycine max), 3'ss of exon 3
----------------gttactatgtctcactttgttaacttgtgtttc---cgccc-attgtccttt-tgctaccatttctaaactc----tgctatttattgtttatttgcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
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gctagtgctatattatggtcttgtacttttctttctagtctagtgtagcaagcgctagattgtttttcatttttctttcttcagacttgtattcttaaataacttctgttattctgtttagAGAACAATTACAATGAGGAAAAAGGAAGGGCTTGCTGATTATCGATATTTTCCAGAACCAGACCTTCCAGCAGTAATCCTTTCTCAAGAATATGTTGATG
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0049g02140.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gttactatgtctcactttgttaacttgtgtttccgcccattgtccttttgctaccat-----ttctaaactctgctatttattgtttatttgcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
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gttgtagctacatccttggtttttccctttattgttttttttttctttttcttttttgtggaatcaatataagaaatgaaattcacatagttgcctcaaggatgcttatttgctctagcaact-tttgttgtaatgtgtagAAAACGGTTACAATGAGAAAGAAGGAAGGTCTTTCCGATTATCGATATTTCCCTGAGCCTGATCTTCCAGAAGTAATTCTTACTGAGGATTATGTTGGTAMapped 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|33797712|gb|CF324715.1|CF324715EST: AGGCTGATCAAATTGTACAAGAAACCCGCCTGTGGGATGAATCTTCTCAG AAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGACTATAGATATTTT
genomic: AGGCTGATCAAATTGTACAAGAAACCCGGCTGTGGGATGAATCTTCTCAGgttactatgt ... gcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtccttttgctaccatttctaaactctgctatttattgtttatttgcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
ttctaaa putative branch site (score: 2)
catcctc putative PPT
tatttattgtttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttactatgtctcactttgttaacttgtgtttccgcccattgtccttttgctaccatttctaaactctgctatttattgtttatttgcatcctcagAAAACTTTTACAATGCGAAAAAAGGAGGGACTTGCTGATTATAGATATTTTCCTGAGCCTGATCTTCCTGAAGTTGTTCTTACTAGTGAGTACATTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG