Sequence
atgc intronic sequence ATGC exonic sequencegtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g03410.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcat-tactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
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-----------------------gtatctac-ttggggccatctgaatctgtcgg--gaatctgataggggcaagtc-tgcagtttagctgaccatt--ttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
upper sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
--------------------------------------gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattac---tgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
| || |||| |||| || || | || | | | | || ||| || | || | ||| | || || || | | ||||| | | || ||| ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||||| |||||| ||| | |||||||| ||||| || || ||
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcc-tatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttc---attactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
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-----gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
upper sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 6
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattactg------tagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
| || | | ||| | || ||||||| | | ||| || | ||| ||| | | | | ||| ||| | || | | || ||||||| || || | ||| || | |||||| ||||| ||||||||||| || ||||| ||||||||||| |||||||| ||| || || ||||| ||||| ||||| || || ||
----gtgagcaaaaatgtgttgatcat---tatctttgtt---tcctttttatccct-cttagcattcaaaatgttcttgcaa-tctttatttgagttatggttttctctctttgcaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGTAAGTCAGGTCCCGAGTCGGATGTATGGAGTATTGGTGT
upper sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
----------------------gtatttatttcaagagcttttgcttatgtgcatcttt-gctatgtgctt--ccaattgttgcttctgatttgagtaggaca----tacaagtctgcagttcattcattgttttctttc-----attactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
| | | || |||| || | ||| ||| | | |||| | ||| | ||| || || | | || | | ||| ||| || ||| || | | || ||| ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||| || ||| | |||||||| ||||| || || ||
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacata-caagtctgcagttcattcattgttttctttcattactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
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------------------------------gttagtagcaaagtgatttaaagtttttctt-------------gacatatcacttctttgatctaaccattatgt------aacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGTMapped 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|29657420|gb|CB653695.1|CB653695EST: CTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG GGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAG
genomic: CTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAGgtatttattt ... attactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagtaggacatacaagtctgcagttcattcattgttttctttcattactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
ttgttttctttcatt CT-rich tract
attgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA