Sequence
atgc intronic sequence ATGC exonic sequencegtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22330.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 5
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
| |||| | || | | | | | | || | | | | ||| | | || | | | | | || || || |||| || |||||||||||||||| || || |||||||||||||| | || ||||||||||| ||||| | || | |||||||| |||||||| || ||||||||||
----------------------------------------------------taagaattaattcttgtatttgcatctcaacatggaggcctcctgtattctatgctc-ttgttctgaagaggaaataacct---cctcatcattttttttg-cagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgat------agGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
| | | || | |||| | | ||| | | || | | | || | | |||||| || || || | || ||| | || ||| ||||||||||||| || || || |||||||||||||||| || ||||||||||| ||||| | || | |||||||| ||||||||||| || |||||||
---------------------------------------------------------gatttttaataagaattaat--gcttgtatttgcgtctcaacatggaggcttcatgtgct--cttgtt-ctgaagaggatctaat-cttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttga-ctgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
| || | ||| | | | ||||| |||||| || | | | || |||| | | | | || || | || | || | ||| || | ||||||| || || || ||||||||||| || ||||| ||||||||||| || || ||||| || ||| ||||||| || |||||||| || |||| || |
-------------------------------------------------agaggcttgta--ctggtgtactct-gtttgaatgtgttctagacattgactata---ttat--atatttcagatttcttattgtgatt-tgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttat-tatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
| | ||| | | | | | || | || | | | ||||| | ||| | | | ||| | | | || | | || | | | ||||||| ||||| || || |||||||| |||||||| || ||||||||||| || |||||| | || | ||||| || |||||||| || |||| || |
-------------------------------------------------ctaaagttacatctttataaggtgtggtttcagagacacagtg-----ggttccccatgttaattattcatcttctcatt--gcttttttcttttctctgtaat--cagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
| || | |||||| | | |||| | | | | || || | | | | || |||| || | ||||| | | | | || | | || | || || |||||||||||| ||||| ||||| ||||| ||||||||||| |||||||| ||||| |||||| | || |||||||||| ||||||||||| || |||||||
-------------------------gttagtgctatgattattatgctcgttgcagtgtagccc------tcttgattc-tttatacagtatcctttgtat---attttatgcttgtaatcttatgcccattt---ctatgtg-ttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 5
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
||| |||| | || | | | || | || || | || | | ||||| |||||||| || ||||| ||||| |||||||| || ||||||||||| || ||||| ||||| ||||||| || |||||||| ||| |||||||
-------------------------------------------------------------------------------------gtactaactgtgaagaaagggtccagt-----ttctcttcacacagcaagtgtgggtgtat-------gtagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 5
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
||| |||| | | || | | | || | || || | || | || | |||| |||||||| || ||||| ||||| |||||||| || ||||||||||| || ||||| ||||| ||||||| || |||||||| ||| |||||||
-------------------------------------------------------------------------------------gtactaactgtgatgaaagggtccagt-----ttctcttcacacagcaagtgggtgtattc---------agGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGMapped 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|116443983|gb|EG486575.1|EG486575EST: ATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAC GATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGC
genomic: ATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttc ... tgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
ttttgac putative branch site (score: 3)
tactttt CT-rich tract
atatactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA