Sequence
atgc intronic sequence ATGC exonic sequence...ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10540.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 10
ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggt-caatgac--tcatgatccttgttctttatgacaatattat-tctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
|| |||| || | | || | | | | | || | || | |||| | || || | | || | | ||| |||| || |||||||||||||||||||| ||||| || ||||| |||||||||||| | ||||| || | || ||||||| || | || |||||||
----tcacctgaagattgtgacacacctgcttccatatcaattaagtagtgctatactgattatgagggtaatttcttttttttttggcatgtgtcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACCAAACAAGATGAAGGATTTGTTTCTGGTATTCGTGGAGTAGAATGGGATG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
----------------ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattat--------tctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
| ||| || | | | | | || | | | | | || | ||| | || || || ||| | | | | | |||| || |||||||||||||||||||| || || |||||||| |||||||| ||| | ||||| || | || ||||| || || | || |||||||
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 10
ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatg-actcatgatccttgttctttatgaca-atattattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
| | | | |||| | ||| | || | | || ||| || | ||| ||||| | | ||| | | | ||||| |||||||| |||||||||||||| ||||||||||| ||||||||||| || | |||||||| || || |||||||| | || ||||||||||
tgataaaatatcaactgatataatacgttactcactagaattagcctaatttgtgcacttatc-tataaattcattatggtttacactatctttttct-cagGTTGAGACTGTTTTCCATGAATTTGGTCATGCTCTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattattctgattt---acagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
| |||| | || | | | || | | | | || | || | | | || || | | | | || || | |||| ||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| || | |||||||| || || |||||||| | || ||||||||||
--cgttactggcaattcttaat-ctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatctttttcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 13
ttccatacttgaaact--ttaggtgcttttggagaactcttacatgcatggtcaatg-actcatgatccttgttctttatgacaatattattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
||| | ||| || | |||| | || || || | || ||| || | | | || | ||| || ||| ||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||| |||||||||| || || ||||||| ||| || ||||||||||
-agtgggggtgatggtggttatgtttatacatagaatatcatcttgttcagtttgtgcatgcacaatc-ttatattgttagata-tatatgcatgttttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 10
ttccatacttgaaact--ttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
||| | ||| || | |||| | || || || | | ||| | | | || | ||| || ||| ||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||| |||||||||| || || ||||||| ||| || ||||||||||
-agtgggggtgatggtggttatgtttatacatagaatatcatcttgttcagtttgtgcatgcgcaatcttatattgttagata-tatatgcatgttttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0061g01070.t01 (Vitis vinifera), 3'ss of exon 10
ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttc-------tttatgacaat-attattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
| || | ||| | |||| | || || | | || ||||||| | | || |||||| ||| | | || ||||| || ||||| |||||||| ||||||||||| |||||||||||| | ||||| | ||||| | || || | ||| || || || |||||||
----ttttttttatcttccgaga----tggaacaatcatatttatcaattttataactcatgcagcatatttagataatcttatgaaaattgatgtcaccataagcagGTTGAAACTGTCTTCCATGAGTTTGGCCATGCCCTTCAGCATATGTTAACCAAGCAAGATGAAAGTCTTGTTTCAGGTTCTCGAGGGATAGAATGGGATGMapped 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|86060879|gb|DR356636.1|DR356636EST: ACCAAACTCCACCTGTTGGTGACAAGCCAAGCCTTATGACATTCCGTGAG GTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACC
genomic: ACCAAACTCCACCTGTTGGTGACAAGCCAAGCCTTATGACATTCCGTGAGgtaaaaaata ... tgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtcaatgactcatgatccttgttctttatgacaatattattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
ttctgat putative branch site (score: 3)
ttattct CT-rich tract
tttatgacaatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattattctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
-tccatac
- - - - ttgaaac
- - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - cttacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaata