Sequence
atgc intronic sequence ATGC exonic sequenceAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22330.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgt----ttaccttctttgacctctcccttctgtgta-gagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|||||| ||||||||||||| || |||| ||||| ||||| || || ||||||||| | |||||||| |||||||| || ||||| || ||||||||||| | ||| ||| | | || | | || | |||| | ||| | ||| ||| | ||| | | || ||| || ||
TGGTAGATGTGATGCTTTTGCTACAGAATACGATCTTGAAGCTGAGGAGTATGTTCCAATCCCCAAAGGGGAGGTCCATAAGAAGAAGGAAATAGTGCAGgtaatttggtgaattttagcctaaaagatttttgcacaggcaagtcttttttgcattg----------tactatctatgaatttatgttggtgataattaaagaaatgaa----------------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|||||| ||||| ||||||| || |||| ||||| ||||| || || |||||||| ||||||||||||||||||| || || || || ||||||||||| | || | | || | ||| | | | || |||| | | | ||| | || ||| | | | ||||| || ||| |||
TGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTGAGGAGTATGTTCCGATTCCCAAAGGAGAGGTCCATAAGAAAAAGGAAATAGTGCAGgt--aatttgatgaatctttgtcttaaggatttt-tgcccatacattttgcacagtcaac-tcttctttgcattgtgctatccattaattaatgtt-gttgataa----------------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|||||| ||||| ||||||| || |||| |||||| ||||| ||||| |||||||| | |||||||| || ||||| || || || || ||||||||||| | | | | | || | | | | |||||||| |||||| || | | || ||| || ||| | | |||| || |
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgt--atcattctgattcaatcttaaccttaacatttcaatattttctgcagtgatttttttcacatggtacctttgttagtgaatgttatcaactta--tcatg-----------------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgt-ttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattat--ctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
||| |||| ||||||||||| || || ||||| || ||||||||||| ||||||||||||||||| |||||||| |||||||| || ||||| || ||||| || || |||| | | | | | | || ||| |||| | ||||| ||| | |||| | | | | | | | | | ||
GGGTCGAAGCGATGCTTTTGCTACCGAGTTTGACCTTGAAGCAGAAGAGTATGTTCCACTTCCCAAGGGAGAGGTTCACAAAAAAAAGGAGATTGTTCAGgtatttaatttgaagaccaatgttatatttatgcaatacctataagatttgataatttagtataattattatatttgaatcc-tctaattgatgctatgag-----------------------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagttt-gtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
||| ||||||||||||| || || || ||||| || ||||| ||||| ||||||||||| || || |||||||| |||||||| || ||||| || ||||| | | ||||| | || ||| |||| || | ||| | | | || || | || ||| |||| ||| | || |||| || |
GGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTGAAGAGTATGTTCCACTGCCTAAGGGAGAGGTTCACAAAAAAAAGGAGATTGTTCAGgt--atttaatttgaatt----------tgaagaccaatt-ttatgtttatgcaataccc--ctaagatttgctaatttagtataattatcatatttgaatcctctaattgatgg-------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|| ||||||||||||||||| || |||||||| || || || ||||| |||||||||||||| ||||||||||| ||||||||||| |||||||| ||||||| || | | ||| ||| | | | | ||| || ||| || || | ||| | || | || | | || | | ||
GGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGGAAGAGTATGTTCCACTTCCTAAAGGAGAGGTTCACAAAAAGAAGGAGATAGTTCAGgtttgtttttgataaattctgggatcttcatgaacca-------tgcttggaacttgatt--ctattgttcatttctcagttgcaatggtatcttgggtgctttgcctt------------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 6
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|| ||||||||||| |||||||| || ||||| |||||||||| || ||||| || | || |||||||| || ||||||||||||||||| || |||||| | || ||| | || || || ||| | || || || || | |||| || | |||| | || ||| | | || ||| | | ||| | ||| |
TGGGAGAAGTGATGCCTTTGCCACAGAGTTTGACTTGGAAGCAGAGGAGTATGTGCCTTTACCAAAAGGAGAAGTTCACAAAAAGAAAGAGATTGTTCAGgttag--tgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattt-tatgcttgtaatcttatgcccatttctatg--tgttatgg-tacatag---------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ33466 (Selaginella moellendorffii), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|| ||||||||||||| || || ||||| || || ||||| || || |||||||| || || ||||||||||| ||||| |||||||| || || ||||| || || ||| | | || | | | | || | | ||||
TGGACGAAGTGATGCTTTCGCGACCGAATTCGACCTTGAAGCGGAGGAGTATGTTCCTCTACCGAAAGGAGAGGTTCACAAGAAGAAAGAAATCGTTCAGgt--actaactgtgatgaaagggtccagtttc---tcttcacacagcaagtgggtgtattcag----------------------------------------------------------------------------------------------
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 5
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgt-tatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
|| ||||||||||||| || |||||||| || || ||||| || || |||||||| || || ||||||||||| ||||| |||||||| || || ||||| || || ||| || || || |||| | | | | || ||||||
TGGACGAAGTGATGCTTTCGCGACTGAATTCGACCTTGAAGCGGAGGAGTATGTTCCTCTACCGAAAGGAGAGGTTCACAAGAAGAAAGAAATCGTTCAGgt--actaactgtga------------agaaagggtccagtttctcttcacacagcaagtgtgggtgtatgtag------------------------------------------------------------------------------------Mapped 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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA