Sequence
atgc intronic sequence ATGC exonic sequence...atatcttgtttgatgaacctttacattgttggcttaattctaatttataattgtgagaatgcttggacaacgtcgattaactgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g35570.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 2
---------------atatcttgtttgatgaacctttacattgttggcttaattctaatttataattgtgag-aatgcttggacaacgtcgattaactgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
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atctacacaacactcaagttttgtttgat-aacttgcacgtcgctttcttagttctggtc-----ttgtaagtgatgtttc----------attaactatcagaatctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGATGAGAAGTACTTGTGGAAAAACTTGACTATTCAGGAAAGTAAAAGGCTT
upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 2
----atatcttgttt---gatgaacctttacattgttggcttaattctaatttataattgtgagaatgcttggacaacgtcgattaac-tgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
|| || || ||| | ||| | | || || | | |||||| | || || || |||| ||| | || || | || | | | | || ||| |||| |||| || ||||| || || || |||||||| |||||||||||||||||||| ||||| ||| | ||| | || || | ||| |||
ttagatgctttagttttggatcaggcttgaaaatgaagg-tgagttctaaatcat-----tgtgattgctggga--atgtttgttgatgtggtggaaatggtgtgtagGTATTTGCAAGATGTGTTTAAGGTTCCTCTGGTTATACAGCTCACTGATGATGAGAAGTTCTTCTGGAAAAATCTTACTATAGAAGAGTGCAGAAGACTT
upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 2
----ata-tcttgttt--gatgaacctttacattgttggcttaattctaatttataattgtgagaatgcttggacaacgtcgattaac-tgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
|| | |||||| ||| || ||| | | || || | | |||||| || | || || |||| || | || || | || | | | | || ||| |||| |||| || ||||| || | || |||||||| |||||||||||||||||||| ||||| ||| | || | || || ||| |||
ttagatgcttttgttttggatcaagcttgaaaatgaagg-tgagttctaaattgt-----tgtgattgctgggg--atgtttgttgatgtggtggaaatggtgtgtagGTATTTGCAAGATGTGTTTAAGGTTCCTTTGGTTATACAGCTCACTGATGATGAGAAGTTCTTCTGGAAAAATCTTTCTATAGACGAGTGCCGAAGACTT
upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ23832 (Selaginella moellendorffii), 3'ss of exon 2
atatcttgtttgatgaacctttacattgttggcttaattctaatttataattgtgagaatgcttggacaacgtcgattaactgtca--gtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
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--------------------------------------------------------gtaggtgtcggcattttttttttttttccatcgcttgcttctgtagATATTTGCAGGATGCTTTCAAGGTTCCGCTTGTCATACAGCTCACAGACGATGAGAAGTGTATGTGGAAGAATCTGAGCGTGGAGGAGACCAAGAGACTT
upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24416 (Selaginella moellendorffii), 3'ss of exon 2
atatcttgtttgatgaacctttacattgttggcttaattctaatttataattgtgagaatgcttggacaacgtcgattaactgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
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----------------------------------------------gtaggtgtcggcattttttat-----ttttttttccatc-gctttcttctgtagATATTTGCAGGATGCTTTCAAGGTTCCGCTTGTCATACAGCTCACAGACGATGAGAAGTGTATGTGGAAGAATCTGAGCGTGGAGGAGACCAAGAGACTTMapped 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|3107892|gb|D42636.1|D42636EST: CGCTGCACCTCGGCCATCTCATCCCCTTCATGTTCACCAA ATATCTGCAGGAT-CTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGA
genomic: CGCTGCACCTCGGCCATCTCATCCCCTTCATGTTCACCAAgtaagcgcga ... cccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGA
EST:
gi|117242702|gb|CT843523.1|CT843523EST: TCGTCGGAGGCGCTGCACCTCGGCCATCTCATCCCCTTCATGTTCACCAA ATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGA
genomic: TCGTCGGAGGCGCTGCACCTCGGCCATCTCATCCCCTTCATGTTCACCAAgtaagcgcga ... cccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataattgtgagaatgcttggacaacgtcgattaactgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
gattaac putative branch site (score: 2)
tatcccttttc putative PPT
attaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatcttgtttgatgaacctttacattgttggcttaattctaatttataattgtgagaatgcttggacaacgtcgattaactgtcagtatcccttttcagATATCTGCAGGATGCTTTCAAGGTGCCCCTAGTAATACAGCTAACTGATGATGAGAAGTTCTTATGGAAGAATTTGACTGTTGAGGAAACTAAAAGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA