Sequence
atgc intronic sequence ATGC exonic sequencegtatgcgctgtatcaccacatacaatatgctttgatcatacatgcaatccaccattcaaagtaaatgactctttctcaacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59350.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G125243_T01 (Zea mays), 3'ss of exon 5
gtatgcgctgtatcaccacatacaatatgctttgatcatacatgcaatccaccattcaaagtaaatg------------actctttctcaa-cagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG
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--gtactct-tatcactatat-catgatacattgatcatgtgt-taatccactgcttaatgtaaatattatttatatatattttttttaaaacagACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAG
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019907_T01 (Zea mays), 3'ss of exon 1
gtatgcgctgtatcaccacatacaatatgctttgatcatacatgcaatccaccattcaaagtaa-atgac-----tctttctc------aacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG
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--gtactct-tatcgctatat-tatggtacattgataat--gtgtaatccactgctgaatgtaatattatctatattttttttgaaaaaaacagACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCCGGAAAAGCCGTTTACGAAAGAAG
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 6
gtatgcgctgtatcaccacatacaatatgctttgatcatacatgcaatccaccattcaaagtaaatg------------actctttctcaa-cagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG----------------------------------------
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--gtactct-tatcactatat-catgatacattgatcatgtgt-taatccactgcttaatgtaaatattatttatatatattttttttaaaacagACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGGTAATTTGGAAGTTGGAAGATTACTGAATCTTTGCTTCTT
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
----------gtatgcgctgtatcaccac-atacaatatgctttgatcatacatgcaatccaccattcaaagtaaatgactctttctcaacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG
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gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcct-----ttgatcaatcttctt---cagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGMapped 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|33793551|gb|CF322658.1|CF322658EST: CCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG ACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTA
genomic: CCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAGgtatgcgctg ... ttctcaacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttgatcatacatgcaatccaccattcaaagtaaatgactctttctcaacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG
ctttgat putative branch site (score: 5)
ctctttctc putative PPT
aaagtaaat 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
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gtatgcgctgtatcaccacatacaatatgctttgatcatacatgcaatccaccattcaaagtaaatgactctttctcaacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG