Sequence
atgc intronic sequence ATGC exonic sequence...tcttggaatatggcttatccttgtggtaaagatggttgtgttgccaccttctttcttgcatttttattgtgaaatttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g38480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G870959_T01 (Zea mays), 3'ss of exon 3
tcttggaatatggcttatccttgtggtaaagatggttgtgtt--gccacct----tctttcttgcatttttattgtgaaatttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
||| ||| ||| || |||| || || | | |||| | | | | || || |||| | || | | | ||||||| |||||||| ||||||||||||||| ||||||| ||||||||| ||||| |||||| ||||||||||||| || ||||| ||||||||||||||
-cttaccgtata--ctatt-ttccaataaatattgtaccctccagtaacctaaaatatataggctgtcttcatgttgaatgtatgtttcatcat--tttgcaacagGGAACTTTACAGTAACAACATAAGTGGGCCAATACCACCTGAACTGGGGAACTTGACTAACCTGGTCAGTTTGGACCTGTACCTCAACAACTTCACTGGC
upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------tcttggaatatggcttatccttg---tggtaaagatggttgtgttgccaccttctttc-ttgcatttttattgtgaaatttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
| | || | | |||| | || | | | || | ||||| | | ||| | | || || || ||| |||| || | ||||||||||||||||| |||||||||| ||| | || |||| | | || ||||| | || ||||| || ||||||||||||||| | |||| |||| | |||
gtaagttccacttatgcatcatgctttaacaaaacaaatccaagatttgacagaagaagcactggagttaccttttgtaattgaaatctttttaacaagtttc-ttattttct-------tacagGGAGCTTTACAGTAACAACATAACTGGCCCGATTCCTAGTAATCTTGGAAATCTGACAAACTTAGTGAGTTTGGATCTTTACTTAAACAGCTTCTCCGGT
upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
--tcttggaatatggcttatccttgtggtaaagatggttgtgttgccaccttctttcttgcatttttattgtgaa-atttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
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agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggatccttttgtgcttaaattattaaattaacttgt---ctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGTMapped 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|44670533|gb|CR283967.1|CR283967EST: TCAGGGGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCT GGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAA
genomic: TCAGGTGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCTgtaagtttac ... ctaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAA
EST:
gi|58588679|gb|CF986987.1|CF986987EST: TCAGGGGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCT GGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAA
genomic: TCAGGTGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCTgtaagtttac ... ctaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttctttcttgcatttttattgtgaaatttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
gactaat putative branch site (score: 2)
atttttattgtgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttggaatatggcttatccttgtggtaaagatggttgtgttgccaccttctttcttgcatttttattgtgaaatttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
- - - - - - - - - ccttgtg
- - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt