Sequence
atgc intronic sequence ATGC exonic sequence...tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgtcaagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56670.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 10
tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgt----caagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
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-ccgtagc-acaaaaaggtgtacctacatgcaagtgattat-gtttgtttagctctgtggtcatggcccctgtttaaaaccaaaaatgaaaattcca-tcacagGTACGTGGAGGTTAATATGAACTCTGGTGCTACTGTTTGGCCACTCTTCAATAGTCTGCAGGCATTCTGGCCAGGGCTTCAG
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 10
tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgt----caagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG------------------
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-ccgtagc-acaaaaaggtgtacctacatgcaagtgattat-gtttgtttagctctgtggtcatggcccctgtttaaaaccaaaaatgaaaattcca-tcacagGTACGTGGAGGTTAATATGAACTCTGGTGCTACTGTTTGGCCACTCTTCAATAGTCTGCAGGCATTCTGGCCAGGGCTTCAGGTTTGGTTACACATATTT
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 9
---------tg-ggtgatgattgcatagtttaattgtacatgttacact----agaggttcttcagctgc---------tttcttgtcaagt----ttcaaata-aaaacctacaattt-------taattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
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gtaaaagcttgtggctatgttgccaccctgtaaatatacttgactcgctgtctatcgttttttgaaatgtgtaagtatgtttatttttaaatgtatttcaagtttgaaactcttgatttgtgtttatgtttcaagGTATGTGGAAGTGAATATGGATTCTGCTGCTATTGTCTGGCCATTATTTAACAGCCTGCAGGCATTTTGGCCTGGCCTTCAG
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------tgggtgatgattgcatagtt---taattgtacatgttacactagaggttcttcagc-tgctttcttgtcaagtttcaaataaaaacc----tacaattttaat-----tccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
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gtaaatgattgtggctatcatgtgctagtatatgaatctacaattccttgactttgttttattcatttattatttattagaattggttttaacccgatcacaaattaggttgggggtttaatttttatgtatctgtagGTATGTGGAGGTAAACATGGATTCTGCTGCTATTGTTTGGCCATTATTTAACAGTTTGCAAGCATTCTGGCCAGGCCTTCAGMapped 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|88361880|gb|CI682051.1|CI682051EST: GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTNTGGCCACTATCCAA
genomic: GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTGgtaaaaatat ... ttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAA
EST:
gi|88394177|gb|CI684850.1|CI684850EST: GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAA
genomic: GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTGgtaaaaatat ... ttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcagctgctttcttgtcaagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
ttttaat putative branch site (score: 3)
tttcaaataaaaacct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgtcaagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
- ggtgatg
- - - - - ttgcata
- - - - - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctaca