Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaaatttggatgcttgttaacatttgtcaattctatggaattatcaataattcagtacatcttgtaattcgatttggttttccttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06820.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 8
gtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaaatttggatgcttgttaacatttgtcaattctatggaattatcaataattcagtacatcttgtaattcgatttggttttccttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
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gtaaattttgtatt--agtttttgcctaccag-taccagata-cttgtcttcttactaat---gtttaatctggcaacaagctaa-gtttgcttgctttacaagataatcgtattgttaaaatgcaccttaatcag--ttgattttttat-agGGAAAGGAGGCTGGGCTGCTCCTCGTCTCAAGGACGCTGTTTTGTCAGATGACAAGTTGCATGAAAGTTACTTTGAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 6
gtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaaatttggatgcttgttaacatttgtcaattctatggaattatca-ataattcagtacatcttgtaattcgatttggttttccttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
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gtaaattttgtatt--agtttttgcctaccag-taccagata-cttgtcttcttactaat---gtttaatctggcaacaagctaa-gtttgcttgctttacaagataattgtattgttaaatgcaccc--taat--aagttgattttttat-agGGAAAGGAGGCTGGGCTGCTCCTCGTCTCAAGGACGCTGCTTTGTCAGATGACAAGTTGCATGAAAGTTACTTTGAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 6
----------gtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaa-atttggatgcttgttaacatttgtcaattctatggaattatcaataattcagtacatcttg-taattcgatttggttttc----cttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
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gttcgctctaatgcattatctgctgttttaatcactgattccaggcatctcttctccattcactctaattcatctgtatatttgactgaaacagagaaatgatgaat--taaagggttttcagttacctaatccaatttactaagaatgttttatttatataattgcagGGAGGGATGGTTGGGCTGCACCGCGTCTCAAGGATGCTGCATTATCTCTAGACAAGTTGCGCGAGTGCTACCTAGAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaaatttggatgcttgttaacatttgtcaattctatggaattatcaataattcagtacatcttgtaattcgatttggttttccttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
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-------------------------------------------ggtttccattaa--aaaagtatggaatttggaatttgg--aattttaaaaaaatgtttttacatctaattgttggagttctcttggtgattgtatttg------tcacagGAAAGGCAGGTTGGGCTGCACCTCGTCTTAAGGATGCTGCTTTATCTCTTGACAAATTGCGTGAAGGTTATGTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggaattatcaataattcagtacatcttgtaattcgatttggttttccttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
tttggttttccttc CT-rich tract
aattatcaataattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacttgtgttttaacatttgtcaattggatgcttgtcaacttctctatctataaaaagggtaaaatttggatgcttgttaacatttgtcaattctatggaattatcaataattcagtacatcttgtaattcgatttggttttccttcagGAAAAGGAGGTTGGGCTGCTCCTCGTCTCAAGGATGCTGCTTTATCTGATGATAAGTTGCGTGAAAGTTATTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT