Sequence
atgc intronic sequence ATGC exonic sequencegtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTTTGCTCTTATGAAGCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52710.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52710.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G094255_T02 (Zea mays), 3'ss of exon 5
gtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagTTA----AGCGAGCTAAGAAG--TACGTATATCATACCTGAGCCTGCCTTTTCTTTGCTCTTATGAAGCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAAC--------------------------------------------------------------
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gtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaagCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCA
upper sequence: LOC_Os04g52710.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
gtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACC--TGAGCCTGCCTTTTCTTTGCTCTTA-TGAAGCTTGCTGGAAAA------AACTCACACCATATTATTGAGGCAAC
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---------------------------taatgattt--ccttaggtagcaacttaaacggatttact--gaaatatttccgtagtctttctacacaagtttgacagaaaatttcaa--tgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAAC--TTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA--Mapped 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|38477762|gb|CF961895.1|CF961895EST: TTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG TTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTT-G
genomic: TTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTTTGCTCTTATGAAGCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAAC
tctttgcttttcctcc CT-rich tract
aacataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTTTGCTCTTATGAAGCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA