Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcttttgttcttgttgttcagaatacgttgtcatttgcacactctgattttaactttgtagatactcatcaattgagtttcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 3
---gtaagtttcttttg----ttcttgttgttcagaatacgttgtcatttgcacactctgattttaactttgtagatactcatcaattgagtt---tcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA
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ggggtttaatgctttgaagatttgcagtggttaagtgtacattctttcgagtttaatatgcttcttacttgtgagctgttaattttatgattgcgatcagGTATCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTCGTGGAGATGTGTCGAGGCATTCAG
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
----gtaagtttcttttgttct----tgttgttcagaatacgttgtcatttgcacactctgattttaactttgtagatactcatcaattgagtt---tcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA
||| | | |||||| | ||| | || ||| ||||| || | | | | | || || | | || ||| | ||||||| || | ||||| ||||||| ||||| |||||||||||||| | | |||| | |||| | |||||||||||||| || ||||| || | ||||
agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtg-agctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtaagtttcttttgttcttgttgttcagaatacgttgtcatttgcacactctgattttaactttgtagatactcatcaattgagtttcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA
| ||||| | | | || | || || ||| || || | ||||| | || | || || |||| |||||||||| | ||||| | |||||||| || |||||||| ||||| | | |||||| |||| | |||||||||||||| |||||||| || | | |||
ggattgtacattatagagacatcagtttgtataaatttttatttttttcatgtaatgt---ttccatgtcttaattttgaattct---gtgttc-tctattg---cccagGTATCTTCTCTGTACAGTTGGATCTGTGTACATCAAATCTAAGGAGGCTCCTGCTAAGGATGTTCTTAAGGATCTTGTGGAAATGTGCCGTGGCATCCAAMapped 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|19874725|gb|AU235556.1|AU235556EST: GCAGAGCTCTACGAGTTAGTTCAGCATGCCGGTAACATTTTGCCAAGATT GTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTAC
genomic: GCAGAGCTCTACGAGTTAGTTCAGCATGCCGGTAACATTTTGCCAAGATTgtaagtttct ... tgagtttcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTAC
EST:
gi|116404335|gb|EG446927.1|EG446927EST: GCAGAGCTCTACGAGTTAGTTCAGCATGCCGGTAACATTTTGCCAAGATT GTATCTTTTATGTACCATAGGATCTGTATATAT
genomic: GCAGAGCTCTACGAGTTAGTTCAGCATGCCGGTAACATTTTGCCAAGATTgtaagtttct ... tgagtttcagGTATCTTTTATGTACCATAGGATCTGTATATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatttgcacactctgattttaactttgtagatactcatcaattgagtttcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA
ttttaac putative branch site (score: 2)
attttaactttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcttttgttcttgttgttcagaatacgttgtcatttgcacactctgattttaactttgtagatactcatcaattgagtttcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT