Sequence
atgc intronic sequence ATGC exonic sequence...atgtaagttgtgatgaaatagtaaatttctcaattcgaacttacatgcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57140.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 8
----------------------atgtaagttgtgatgaaatagtaaatttctcaattcgaacttacat--gcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
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gtatttatctatctcttgaactctatatttattagtctgtcgatatattta-caatttgcgttcacattggtaaagcctcgttagaact-ctagcttacctgagtactctgt--ttgattccagGAACACTTATCAAAGGACGATGCACGGCAACAATTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCTGTTTTCTTCAGTGTTCGGAAGATTGATG
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 9
----------------------atgtaagttgtgatgaaatagtaaatttctcaattcgaacttacat--gcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
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gtatttatctagctcttgaactttatatttattagtctatcaatatattta-caatttgcgtccacattggtaaagcctcattagaact-ctagcttatctgagtactccgt--ttgatttcagGAACATTTATCAAAAGACGATGCACGGCAACAATTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATG
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
--atgtaagttgtgatgaaatagtaaatt-tctcaattcgaacttacatgcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
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tggtttttcttgtggtccttttttaaatgatctcaaaattt-catccataaagaagatgatgacaatatttcttttgatttaat--tatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATGMapped 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|58671897|gb|CK060583.1|CK060583EST: GTCTCACGCTATCAGTTAATG GAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGG
genomic: GTCTCACGCTATCAGTTAATGgtatttacct ... ttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
gcttgat putative branch site (score: 5)
tttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtaagttgtgatgaaatagtaaatttctcaattcgaacttacatgcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - tgatgaa
- - - - - - - - - - - - - - - - - - - - -tacatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttt