Sequence
atgc intronic sequence ATGC exonic sequencegttgggttttgtaaactacatttaatatgtcaaggtgtatctacctatacgtttctaactggaaatcaattttgtttagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60410.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60410.5 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 8
---------gttgggttttgtaaactacatttaatatgtc-aaggtgtatctacctatac-----gttt---ctaactggaa-atcaattttgtt--tagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
|| || |||| | | || ||| || ||| | | | | |||| |||| ||| ||| | | | | |||| ||| |||||| ||||| |||||||| ||||||| || |||||||||||||| || ||||| || |||| || ||||
gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgtttatactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
upper sequence: AT5G60410.5 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G15880.1 (Glycine max), 3'ss of exon 9
gttgggttttgtaaactacatttaatatgtcaaggtgtatctacctatacgtt-----tctaactggaaatcaattttgtttagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
||||| || | || | ||| || | |||| |||| | || ||| ||| ||| ||| | |||||||||||||||||| |||| || || |||| || |||||||| ||||| |||||| | || |||||||||||||
gttggtttggattttctgtgcatg-tataataatgcatatccttctatgcattggttttcttactaaaaa--aatgacttgtagGCTTGGTGTATGCTCCTGAACGACAAGGTTCCATTCAGGATGCAATGGCCACAGTATACAGACCTGCAGGTCAATG
upper sequence: AT5G60410.5 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 9
----gttgggttttgtaaactacatttaatatgtcaaggtgtatctacctatacgttt-ctaactgg--aaatcaattttgtttagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
||| || ||| | | | || || || | | |||| || |||| || ||| || ||| | |||||||||||||||||| |||| || || |||| || |||||||| ||||| |||||| | || |||||||||||||
gtttgtttggattttcagtgcatgtatattaatgcatattct-tctatgcattggtttgcttacttattgaacaaatgacttgtagGCTTGGTGTATGCTCCTGAACGACAAGGTTCCATTCAGGATGCAATGGCCACAGTATACAGACCTGCAGGTCAATG
upper sequence: AT5G60410.5 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0004g03180.t01 (Vitis vinifera), 3'ss of exon 8
---gttgggttttgtaaactacatttaatatgtcaagg---tgtatctacctatacgt-ttctaactggaaatcaattttg---------tttagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
| | || |||| | | | | | | | ||||| | |||| | |||| | || | || ||| |||||||||||||||| ||| | ||||| || ||| ||||||||||||||||| || ||||| || || || |||||||
gttggttagtgccttaaatgatgtctggtgaatttatgatttgtattgagttatagatgttctgattgtttctttatgttgaaattattttttagGCTTGGTGTATTCTCCTTAATGACAAGGTTTCATTTAGGATGCAGTGGCCACAATATGCAGACCTACAAGTCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgtcaaggtgtatctacctatacgtttctaactggaaatcaattttgtttagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
ttctaac putative branch site (score: 1)
ttttgttt putative PPT
aaatcaattttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttttgtaaactacatttaatatgtcaaggtgtatctacctatacgtttctaactggaaatcaattttgtttagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG