Sequence
atgc intronic sequence ATGC exonic sequencegtactaaacactgaaattcaaatcctgaaccaaaagtgcttaattatagagttatgaacttattatgaacttggattttctggatcagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61000.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
gtactaaacactgaaattcaaat-------cctgaaccaaaagtgcttaattatagagtta---tgaacttattatgaacttggattttctggatc-----------agCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
||| ||| |||| ||| |||| | ||| | || | |||| | || ||| | || | ||| | | || ||| | ||| ||||| |||||| |||| || || ||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
----------------------gtactaaacactgaaattcaaatcctgaaccaaaagtgcttaattatagagttatgaacttattatgaacttggattttctggat-cagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
|| |||| | | || | | | ||||| | | ||| | ||| | || | || | | || || ||| | |||||| ||||| |||| || || ||||||||||||||||| || || |||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtaataattactgtcattagaataacctaacatgatcaacctggtctt--agccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0587g00010.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtactaaacactgaaattcaaatcctgaaccaaaagtgcttaattatagagttatgaacttattatgaacttggattttctggat-cagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
|| |||| | | || | | | ||||| | | ||| | ||| | || | || | | || || ||| | |||||| ||||| |||| || || ||||||||||||||||| || || |||||||||||||||| ||||||||||| || ||||||||||| |||| |
gtaataattactgtcattaaaataacctaacatgatcaacctggtctt--agccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGGTG
upper sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 9
gtactaaacactgaaattcaaat--cctga----accaaa--agt----gcttaattatagagttatgaacttatt--------atgaacttggattttctggat-cagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
||| ||| |||| ||| |||| | | | |||||| || || || | | |||||| | | |||| || | | || || ||| | |||||| ||||| |||| ||||| ||||||||||||||||| || || |||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtaataattactgtcattaaaataacttaacatgaccaaactggtcttagccaaagttttgagttaaaaccatattcagttttgataatgtgggcttgtctctgtacagCCTTCCTTTTTTAGCATCAGGGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
gtactaaacactgaaattcaaat-------cctgaaccaaaagtgcttaattatagagtta---tgaacttattatgaacttggattttctggat-----------cagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
||| ||| |||| ||| |||| | ||| | || | |||| | || ||| | || ||| | | || ||| | ||| |||||| |||||| |||| || || ||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATGMapped 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|86084110|gb|DR379869.1|DR379869EST: GAGTGCTTCTCTCTCACATCACAAGCAATCCATCTTTATTCGAAGAAAAG CCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAA
genomic: GAGTGCTTCTCTCTCACATCACAAGCAATCCATCTTTATTCGAAGAAAAGgtactaaaca ... tctggatcagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtgcttaattatagagttatgaacttattatgaacttggattttctggatcagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
gcttaat putative branch site (score: 4)
ttttct putative PPT
ttaattatagagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaaacactgaaattcaaatcctgaaccaaaagtgcttaattatagagttatgaacttattatgaacttggattttctggatcagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA