Sequence
atgc intronic sequence ATGC exonic sequence...tttatcttggtatgcatgcaaacgccttcagtttttttttcattgtatataactatattagtgactgcacaatcattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40070.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G366434_T02 (Zea mays), 3'ss of exon 3
tttatcttggtatgcatgca----aacgccttcagtt---tttttttcattgtatata-------actatattagtgactgcacaat--cattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
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-----cttggtatgcattcaccttagctcctgcccttacatttttgttgttgtatagatcttcctattttaacaatcattttgctatgccattgtatatccactgTATACACTTAGGTGGCTATGACAAGGAGGACAAGGCAGCAAGGGCTTACGATTTGGCAGCTCTCAAGTATTGGGGCACTACGACAACAACAAATTTCCCT
upper sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G366434_T01 (Zea mays), 3'ss of exon 3
tttatcttggtatgcatgca----aacgccttcagtt---tttttttcattgtatata-------actatattagtgactgcacaat--cattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
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-------tggtatgcattcaccttagctcctgcccttacatttttgttgttgtatagatcttcctattttaacaatcattttgctatgccattgtatatccactgtaTACACTTAGGTGGCTATGACAAGGAGGACAAGGCAGCAAGGGCTTACGATTTGGCAGCTCTCAAGTATTGGGGCACTACGACAACAACAAATTTCCCT
upper sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G38370.1 (Glycine max), 3'ss of exon 1
tttatcttggtatgcatgcaaacgccttcagtttttttttcattgtatata-actatattagtgactgc--acaatcattatacttgtatcacgactact--cagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
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-ttaaatta-taattgtattattatttt---ttttgggccaaaagtaagaagagaacgttaaaatttgtttacatttggttatcatttgttgtcactacttgcagGTGGTTATGATAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACCACAACAACAAATTTTCCA
upper sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G31440.1 (Glycine max), 3'ss of exon 5
tttatcttggtatgcatgcaaacgccttcagtttttttttcattgtatata----actatattagtga--ctgcacaatcattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAAC---AACAACAACAAATTTCCCA
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-----ttagaaaaagaaataaaaacattttttcctcatcataatattaatatcacattattttagttgttcttcacaaataccat-ttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
upper sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g00950.t01 (Vitis vinifera), 3'ss of exon 3
----tttatcttggtatgcatgcaaacgccttcagtttttttttcattgtatataactat-attagtgactgcacaatcattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
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ttgttttctctttttattcttttat-caaacctatatttccgttcagatttcttaactaccactgttgttttctttgtttttgtttttgtttttc----ccatagGTGGTTATGACAAAGAAGAAAAGGCAGCTAGGGCTTACGATTTAGCAGCACTGAAGTATTGGGGTACCACCACCACAACAAATTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatataactatattagtgactgcacaatcattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
atataac putative branch site (score: 3)
aactatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatcttggtatgcatgcaaacgccttcagtttttttttcattgtatataactatattagtgactgcacaatcattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAACAACAACAACAAATTTCCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - tgcatgc
- - - - - - - - - - - - ccttcag
- - - - - - - - - - - - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtat