Sequence
atgc intronic sequence ATGC exonic sequencegtaatattgttttacttttcttggaaatgttaccccatcttgcattgcatgtgttgcctgctaatattagtttctttatattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g10690.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g10690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G090935_T01 (Zea mays), 3'ss of exon 5
gtaatattgttt-tacttttcttggaaa----tgttaccccatcttgcattgcatgtgttgcctgctaatattagtttctttatattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
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gtacccttatttgcccttcttttggaaaatgatgccttccaacgatgcatcctttatgttgctcactgatat--atttcggtaaaatgcacagGAAACTGAAGAAGCAGAACTCAAAATGCTGAGAAAGAGTTTGAACTTCAAGGCAACACCAATGCCAAGCTTCTATAAGGAACCAACTCCTGTCAAGGTTG
upper sequence: LOC_Os02g10690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G452633_T03 (Zea mays), 3'ss of exon 6
gtaatattgttttacttttctt--ggaaatgttacc--ccatcttgcattgcatgtgttgcctgctaatattagtttctttatattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
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gtacccttatttgcccttcttttgggaaatgctgccttccaacatacatctcttatgttttttgctgatat--atttctgtaaaatgcacagGAAACTGAAGAAGCAGAACTCAAAATGCTGAGAAAGAGTTTGAATTTCAAGGCAACACCAATGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTG
upper sequence: LOC_Os02g10690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G32330.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaatattgttttacttttcttggaaatgttaccccatcttgcattgcatgtgttgcctgct--aatattagtttctttatattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
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-----gttgtctcctatacccaccctgtttattgtcatagtgt-ttagatgcttggcctcctccaaaacaaaattcttggtttctcgcagGAAACACAAGAAGCTGAGCTTAGGATGCTAAGGAAGAGTTTGAACTTCAAAGCCACACCTATGCCTAGCTTTTATCAAGAACCTCAGCCGCCTAAAACAG
upper sequence: LOC_Os02g10690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
gtaatattgttttactttt--cttggaaatgttacccc----atcttgcattgcatgtgttgcctgctaatatt------agtttctttat-attgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
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gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGGMapped 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|163929122|gb|EG710979.1|EG710979EST: AGATTCATGCCAGAGAAATGGAAATAAGCAATTTGCAAGCAAAATCAAAG GAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAG
genomic: AGATTCATGCCAGAGAAATGGAAATAAGCAATTTGCAAGCAAAATCAAAGgtaatattgt ... tattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAG
EST:
gi|4714336|gb|AU058303.1|AU058303EST: AGATTCATGCCAGAGAAATGGAAATAAGCAATTTGCAAGCAAAATCAAAG GAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAG
genomic: AGATTCATGCCAGAGAAATGGAAATAAGCAATTTGCAAGCAAAATCAAAGgtaatattgt ... tattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccatcttgcattgcatgtgttgcctgctaatattagtttctttatattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
tgctaat putative branch site (score: 2)
tttctttat putative PPT
taatattagtttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatattgttttacttttcttggaaatgttaccccatcttgcattgcatgtgttgcctgctaatattagtttctttatattgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC