Sequence
atgc intronic sequence ATGC exonic sequencegtattagaaacaactctggattctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g48790.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G114192_T01 (Zea mays), 3'ss of exon 4
--------------gtattagaaacaactctggattctttc--gttagaa--aagcatacacatacactaa-cctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
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gttaactgacacgcgtcttacta-tgtcttcagattatacaaggttcatattatacctacacatacgctaatcctggtgcatttctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTCCTCAAGACCTTAATCTTGAAGACTCTAAAGGAACGAAACAAAAAGGATG
upper sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
---------------------------gtattagaaacaactctggattctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
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ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcac-tatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
upper sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
----------------------------gtattagaa-acaactctggattctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
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tttcttcctaccagtgaggcccgtataactgtttgtatgcacatgttacttatgctagtggatgtggatatttaaatgtttgttt-cattgt--gctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
upper sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0048g02830.t01 (Vitis vinifera), 3'ss of exon 5
----------gtattagaaacaactctgga-----ttctttcgttagaaaagcatacacatacactaacctgcaatgtttgttt-----------tccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
||| | ||| || | | || | || || | || |||| | |||| |||||| | |||||||||||||| ||||||||| |||| ||||| || || || ||||| ||||| |||||| |||| ||||||| | | |||||||| | | | |
attggcatgtgtagttaaaatggctattgtgaaattttccttctttcaagacaatttggctacagtgtaagtaaatgattgtttattttgtttgatacagATGGCCGATCCTTTGACTGCCTTGATTCATGCGGTGCAAGTTATGAACTTCCTTAAGACACTGATTATGAAGACCCTTCAAGAAAGAGAAGAATCAGCTG
upper sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------gtattagaaacaactctggattc-tttcgttagaaaagcat-------acac-atacactaac-----ctgcaatgtttgt-tttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
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gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATACMapped 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|25807183|gb|CA763144.1|CA763144EST: TGGTCTTTGCGCCAAACATGACTCAG ATGGCCGATCCATTGACTGCCNTGATACATGCAGTTCAGGTCATGAATTTC
genomic: TGGTCTTTGCGCCAAACATGACTCAGgtattagaaa ... tgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTC
EST:
gi|33381851|gb|CF197194.1|CF197194EST: AGATGAATGCTAGAAACATCGCTATGGTCTTTGCGCCAAACATGACTCAG ATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCANNTCATGAATTTC
genomic: AGATGAATGCTAGAAACATCGCTATGGTCTTTGCGCCAAACATGACTCAGgtattagaaa ... tgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
cactaac putative branch site (score: 1)
tttgttttcc putative PPT
ttagaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagaaacaactctggattctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG