Sequence
atgc intronic sequence ATGC exonic sequence...taccacattattttcttcacagaatacaactgttatacatgttcctttttctgtttattttcataatggctgaatttgagtaattaatgttccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38710.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G099481_T01 (Zea mays), 3'ss of exon 4
--taccacattattttcttcacagaatacaactgttatacatgttcctttttctgtttattttcataatggctgaatttgagtaattaatgttccatat-cagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
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tttaccacatc--ttcctctgtggtgtgttgttgatatgcatgctt-ttctgctgtaaatggccaaaagtgttaaatgcgattacttaatgttacatgttcagGTCTGACGTGCTGGGTCAGGTCATGCCTTTGGTTGGACGTGATTGGAGTCACTCAGGTGTTGCTCGCCTTTTTTCTGCAATTAAG
upper sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G19730.1 (Glycine max), 3'ss of exon 4
-----taccacattattttcttcacagaatacaactgttatacatgttcctttttctgtttattttcataatggctgaatttgagtaattaatgttccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
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agttctgctaaaataatctatggagggagtagaa--gacagagttgcattatggtttgagaaccatgataaaaactttgttt---ttttttttctttccttttagGTCTGATGTTTTGGGGCAGTTCATGCCTTTAGTTGGCAAAGATTGGACACAATCTGGAGTGGCAAGGCTTTTCTGTGCTATTAAG
upper sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G05320.1 (Glycine max), 3'ss of exon 4
-taccacattattttcttcacagaatacaactgttatacatgttcctttttctgtttattttcataatggctgaatttgagtaattaatgttccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
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tgaatggaagttgtgtaaaataatctatggagggagtaaaaggccgagttgcattatggtttgagaacca-tgataaaaactgttttttctttccttttagGTCTGATGTTTTGGGGCAGTTCATGCCTTTAGTTGGCAAAGATTGGACACAATCTGGAGTGGCAAGGCTTTTCTGTGCTATTAAG
upper sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0040g02800.t01 (Vitis vinifera), 3'ss of exon 3
--taccacattattttcttcacagaatacaactgttatacatgttcctttttctgtttattttcataatggct---gaatttgagtaattaatgttccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
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acagctatagtagatctagttttgactttg--cattgtggtggctcacaatcaaatatagatttgacgtggctcatgaattaccctaatgtgtgtttt---tcagGTCTGATGTTCTAGGTCAGTTCATGCCTTTAGTCGGAAAAGATTGGACTCAATCTGGGGTTGCTCGACTTTTCTCGGCCATTAAGMapped 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|33796855|gb|CF324291.1|CF324291EST: AAAACATTGTAACTTTTAGCTTCTCCACCAGAGTTCTTGGAAAGCAACAG GTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCA
genomic: AAAACATTGTAACTTTTAGCTTCTCCACCAGAGTTCTTGGAAAGCAACAGgtctgtgccc ... tccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttctgtttattttcataatggctgaatttgagtaattaatgttccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
aattaat putative branch site (score: 3)
tgtttattttcataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taccacattattttcttcacagaatacaactgttatacatgttcctttttctgtttattttcataatggctgaatttgagtaattaatgttccatatcagGTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG