Sequence
atgc intronic sequence ATGC exonic sequence...caactaatactgcagtagtgcacttgttcttaggcaaaagaacgaattctgttggtagcaagttgagtgttgatcgctcttgttgcttgttgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g65090.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G400604_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------caac-taatactgc-agtagtgcacttgttcttaggcaaaagaacgaat-tctgttggtagcaagttgagt-------gttgatcgctcttgttgctt-----gttg--tgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
||| |||| | | ||| | |||||| | | || | |||| | | ||| || ||| ||| || | | | | ||||||||||| ||| | ||| |||| |||||| ||||||||| | ||||||||||||| |||||||||||||||||||||||||||||||| |||||||| || | ||||||||| |
gtgaggggtgcaattagcccgcggtataatttcctacagtgagaataacactgaatgcagttgttaaataaaacataatctttctagttgaacacttgatttagatattcagcaagaatgtgtcttgttatcaaattgggttatttcaggtaaacattcttgttgcttacctagttaccttatccagGCCGGGATGGATGCAATTAGGAATGGTTATACAAGATACACTCCTAATGCTGGGACTTTGGAGCTGAGGAAGGCTATTTGTACTAAACTCCAGG
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G400604_T02 (Zea mays), 3'ss of exon 2
caactaatactgcagtagtgcacttgttcttaggcaaaagaacgaat-tctgttggtagcaagttgagt-------gttgatcgctcttgttgctt-----gttg--tgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
| | |||||| | | || | |||| | | ||| || ||| ||| || | | | | ||||||||||| ||| | ||| |||| |||||| ||||||||| | ||||||||||||| |||||||||||||||||||||||||||||||| |||||||| || | ||||||||| |
---------------ttgaacacttgatttagatattcagcaagaatgtgtcttgttatcaaattgggttatttcaggtaaacattcttgttgcttacctagttaccttatccagGCCGGGATGGATGCAATTAGGAATGGTTATACAAGATACACTCCTAATGCTGGGACTTTGGAGCTGAGGAAGGCTATTTGTACTAAACTCCAGG
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G400604_T03 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------caac-taatactgc-agtagtgcacttgttcttaggcaaaagaacgaat-tctgttggtagcaagttgagt-------gttgatcgctcttgttgctt-----gttg--tgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG------
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gtgaggggtgcaattagcccgcggtataatttcctacagtgagaataacactgaatgcagttgttaaataaaacataatctttctagttgaacacttgatttagatattcagcaagaatgtgtcttgttatcaaattgggttatttcaggtaaacattcttgttgcttacctagttaccttatccagGCCGGGATGGATGCAATTAGGAATGGTTATACAAGATACACTCCTAATGCTGGGACTTTGGAGCTGAGGAAGGCTATTTGTACTAAACTCCAGGGTGTGT
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0031g00980.t01 (Vitis vinifera), 3'ss of exon 2
----------caactaatactgcagtagtg-cacttgttcttaggcaaaagaacgaattc-tgttggtagcaa----gttgagtgttgatcgctcttgttgcttgttgtgat-ctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
|| | || | | ||| ||| ||| || | | | | | || | |||| || || || | || | || ||||||||||| ||||||||| || ||||| |||||||||||||| ||||| || |||||||| | | || || || |||| | | |
gttttctttttgacctttttcaatttaatctcttttggtctgtggctaatgtgtttacctatacttacaccactgatactatctgttcttctcttctgatatttttgaaaatgttagGCTGGGATAAATGCAATTCGTGAAGGTTACACAAGGTACACTCCAAATGCGGGTACTTTGGAAGTCCGTTCAGCAATTTGTCATAAGTTGAAGG
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g04860.t01 (Vitis vinifera), 3'ss of exon 2
----------caactaatactgcagtagtgcacttgttcttaggcaaaagaacgaattctgttggtagcaagttgagtg-ttgatcgctcttgttgcttgttgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
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gttacctatccttttcttcccaatttggcaaaaatttctgtttttccttttttattttttccttttctttacttgtatggttcatcgtttttttttttggtgtaaatttagGCTGGGATAAATGCAATTCGTGAAGGTTATACAAGGTACACACCCAATGCAGGCACTCTGGAGCTCCGCACTGCAATTTGTCATAAACTAAAGGMapped 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|88396984|gb|CI578133.1|CI578133EST: GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAG GCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
genomic: GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgcct ... tgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
EST:
gi|29645872|gb|CB650879.1|CB650879EST: GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAG GCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
genomic: GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgcct ... tgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctgttggtagcaagttgagtgttgatcgctcttgttgcttgttgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
tgttgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caactaatactgcagtagtgcacttgttcttaggcaaaagaacgaattctgttggtagcaagttgagtgttgatcgctcttgttgcttgttgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA