Sequence
atgc intronic sequence ATGC exonic sequencegtagacatcggaagcttcacacatcttaagcaccttgttacatgcggaactgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g37837.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
gtagacatcggaagcttcacacatcttaagcaccttgttacat-gcggaactgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
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---------gtaataatca-gtatgttgtgatctttataacctagtttgtcctccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
upper sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 7
------------gtagacatcggaagcttcacacatcttaagcaccttgttacatgcggaactgtct-tttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
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ttgcgtttagattgatgtattggttggtctaacctaaattgacatctttcttttcccaagtttatttgtttctcgtgtgattaaattttatttac------tgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGATGCTGCAGCAAAGAAGTATGATCTAGAAGCATGGTTTCCAGCCTCTCAAG
upper sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G29600.1 (Glycine max), 3'ss of exon 7
-------gtagac--atcggaagcttcacacatcttaagc-accttgttacatgcggaactgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
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attgtgtgtagattgatgtattggttggtctgacttaaattgacttctttctctcccca-tgttttttgtttctcatgtgattaaattttatttactg--cagTTAAATCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCATTGAATGATGCTGCAGCAAAGAAGTATGATCTAGAAGCATGGTTTCCAGCCTCTCAAG
upper sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0128g00370.t01 (Vitis vinifera), 3'ss of exon 7
--gtagacatcggaa--gcttcacacatcttaagcaccttgttacatgcggaa---ctgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
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atgaaagaaatggatctgctcttgtgatatgatgattattccttagtgaagaatgcccttttttccgccctggaatgtaactccatttcctctattacagCTAAACATTCCCTATCAAGTTGTTGCCATTGTTTCTGGTGCCTTGAATGATGCAGCTGCAAAGAAGTATGATTTGGAAGGATGGTTCCCTGCATCCCAGAMapped 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|27577321|gb|CB000016.1|CB000016EST: GGGAGATGCATGAAGAAATGATAAAAAATTCAGAAGATTTCTACAAGGAG ATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGAT
genomic: GGGAGATGCATGAAGAAATGATAAAAAATTCAGAAGATTTCTACAAGGAGgtagacatcg ... tattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGAT
EST:
gi|163925426|gb|EG713339.1|EG713339EST: GGGAGATGCATGAAGAAATGATAAAAAATTCAGAAGATTTCTACAAGGAG ATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGAT
genomic: GGGAGATGCATGAAGAAATGATAAAAAATTCAGAAGATTTCTACAAGGAGgtagacatcg ... tattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatgcggaactgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
gtctaat putative branch site (score: 3)
tttcttcattgtct putative PPT
taatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagacatcggaagcttcacacatcttaagcaccttgttacatgcggaactgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC