Sequence
atgc intronic sequence ATGC exonic sequencegtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23990.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
------gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattct------cagcatat----ccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
| | || | |||| || ||| || | | ||| | |||| || || | | ||| | | | ||| | |||||| | | || |||| || || || |||||||||||||||||||||||||| ||||| ||||||||| ||||| || || ||| |||
gtatgaatgattcctagaaggctggtagata-agctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------gtagcctttgaaaccttaactgatatagacatggtg-gctcttagtatgaactagatttgg----ctattacattctcagcatat-ccttgttggattgtaagtgtagttgagacttgtctggctatttg-tatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
| | |||| | |||||| | | | | | || ||| | | | || || || | ||| | | ||| || | | | | || || || || || || || |||| || ||||| ||||| |||||||||||||||||||| ||||| ||||| || ||||| || || || |||
gtatagtagatgatttaaaaggatttttctattgatttggattgcagcaaccttc--agccttaagtcacagtattctaacatgagctcagtgttgtgcaagtaccaaaatctgttgtgtttgta-catgtgctttgatgtaatactattttatgtgctgaatgacttccttttcaatacagGTGACTGTCTCTAAGGATGACACTGTTATTCTTGATGGCGCTGGAGACAAAAAGTCTATTGAAGAGAGGGCAGACCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 11
gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
| | | ||| | || | || || ||| | | ||| || || | || | | || | || | | | ||| ||| | ||| | || || || |||||||| || |||||||| ||||| || ||||||| |||||||||||||||||| |||
-----------------------ttttctcctggagcaactgcttgtgtttaagctttaaaaaaaagtttcattaaatttcactattctttgcccatactaaataaggttcttta---tgttt---tagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 11
gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgt-tggattgtaagtgtagttgagactt-gtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
|| | | || | || | ||| | ||||| | | | || | | | | ||| | ||||| | | || | | || | ||||| || ||||| |||||||| ||||||||||| || || |||||||||| | ||||||||||||| || |||
-------------------------------tgtgtgatattggaatatgttttcattgagttcatcattcgtatcctgatactgcatagggttaacgtggacaactgacttaggttcataatgtttgcagATAACAGTTTCTAAGGATGACACTGTCATTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 11
gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
||| |||||| | || | | || | || ||||| | | || || |||| || | | || | || | || | | | | | ||| | ||||| || ||||| |||||||| |||||||| || || || |||||||||| | ||||||||||||| || |||
-------------tcttgtttgatattggaatat--attttcagagtt--cttcatttgtatcctg-atactt--catagggttatcg---tggacaactaacttaggttcat------aatgttgtagATAACAGTTTCTAAGGATGACACTGTCATTCTTGACGGAGCAGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 11
gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
| ||| ||| | | | |||| || |||| | || | || | ||| | || ||| | | || | | || | | | ||||||||| | || |||||||| |||||||| |||||||||||||| |||||||| | ||||||||| | ||||| |||
--------------tccgaatga-atatatgttttaactctaggtta----tagaatgaactgcaccctttgtattatacaggtctt---ttgca-gcataactaa------ctaggttcatgttttagGTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
tatttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG