Sequence
atgc intronic sequence ATGC exonic sequence...tatgtgtttcattcttctaatgtatccattagactggagactgaaaaaagcttgcaaagttaccaaaagaacacctgtgttgatcagttttcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71790.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G15910.1 (Glycine max), 3'ss of exon 3
tatgtgtttcattcttctaatgtatccattagactggagactgaaaaaagcttgcaaagttaccaaaagaacac-ctgtgttgatcagttttcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
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---------------------------gtctaactgaatacaattattgagctattttgtt-ttaaaacaatatgcaccattaatggataatatcat--agGTATTATGAAGGTGGCATTTCATCAGTTTACATGTGGGAAGATGATAATGAAGGTTTCGTAACCAGCTTTTTAATAAAGAAAG
upper sequence: AT1G71790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G31170.1 (Glycine max), 3'ss of exon 3
tatgtgtttcattcttctaatgtatccattagactggagactgaaaaaagcttgcaaagttacc-------aaaagaacacctgt-gttgatcagttttcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
||| | | || | ||| | | | ||| | ||| || || || |||| || | || || | | | | ||||||||||||||||| || || ||||| ||||||||||| |||||||||||||| || || || || || | || |||||||
-----atttaactattttg-tgtgttcgtcttgctgtctatataaattcaattatttagctattttgttttaaaacaatatgcaccattaatggataatgtcat--agGTATTATGAAGGTGGCATTTCATCAGTTTACATGTGGGAAGATGATAATGAAGGTTTCGTAGCCTGCTTTTTAATAAAGAAAG
upper sequence: AT1G71790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G36400.1 (Glycine max), 3'ss of exon 3
-------tatgtgtttcattcttctaatgtatccattagactggagactgaaaaaagcttgcaaagttaccaaaagaacacctgt-gttgatcagttttcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
| | ||| | ||||||| | || || ||| | || | | ||| |||| || | || || | | | | ||||||||||||||||| || || ||||| ||||||||||| |||||||||||||| || || || || || | || |||||||
atgatcatgtttgtgttgttcttcttgc-tgtctat----ctgaatacaattattgagctattttgtt-ttaaaacaatatgcaccattaatggataatatcat--agGTATTATGAAGGTGGCATTTCATCAGTTTACATGTGGGAAGATGATAATGAAGGTTTCGTAGCCTGCTTTTTAATAAAGAAAG
upper sequence: AT1G71790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g01970.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------tatgtgtttcattcttctaatgtatccattagactggagactgaaaaaagcttgcaaa------gttaccaaaagaacacctgtgttga----tcagttttct------tttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
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gtgaggtcctttacttacctcgtacttgagttcattcctttgataattttgacatgaaaaataatctattttccagatcctttttgcattcctctcattttcaaaagaagcacaaaattagcatttcaattaaccaataaattggtagGTATTATGAAGGTGGCATTTCATCAGTTTATATGTGGGAGGACGAGAATGAAGGATTTGTGGGCTGCTTCTTAATAAAGAAAGMapped 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|164204875|gb|ES165068.1|ES165068EST: CTTGAAGTTGAAGCCAACGATATCTTTGCGATCTATCGTGACCG GTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGA
genomic: CTTGAAGTTGAAGCCAACGATATCTTTGCGATCTATCGTGACCAgtgaggttct ... tcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagcttgcaaagttaccaaaagaacacctgtgttgatcagttttcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
tgttgat putative branch site (score: 4)
tcagttttcttttcc CT-rich tract
ttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgtgtttcattcttctaatgtatccattagactggagactgaaaaaagcttgcaaagttaccaaaagaacacctgtgttgatcagttttcttttccagGTATTATGAAGGTGGTATATCTTCAGTCTACATGTGGGAGGATGATAATGAAGGCTTTGTGGCATGTTTCCTTATCAAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacacc