Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtttggttgctttatgttttataatatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36160.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 25
-----gtgcgtttggttgctttatgtttt---ataatatttttgtctacactctcaactaatgatcagtttgtgtgt--------gtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
||| | | || | || | ||| || | | | | | ||||||| || | | ||||||| || || || ||| || | |||||||| |||||||||||||| || |||| | |||||| |||||||||||||| | | ||| || | |
gtgcggtgattagaaataacctagatattccccttataaattattttgatattttacctaatgaattccatgcatcttaataaacacagTTGGCCCTTAAAGCAAGTGAACTTCTTGAACAAACCAAACTAAGTGAACTCTGTTCCAGCATTGCAAGAAGCCTTTCAGATCTGGGGATGCATAAGGGAG
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 25
---------------gtgcgtttggttgctttatgttttataatatttttgtctacactctcaactaatgatcag-----tttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
| || | | | | | ||||||| | ||| || | | | | | || || | ||||||| || || || ||| || | |||||||| |||||||||||||| || ||| ||| | |||| ||||||||||| || | | ||| || | |
gtgcagtggttagaaataacttagatagatattcccattataatttattttgatatttttcctaatgaattccatgcatcttaataaacacagTTGGCCCTTAAAGCAAGTGAACTTCTTGAACAAACCAAACTAAGTGAACTCCGTGCAAGCGTTGCAAGAAGCCTTTCGGATCTGGGGATGCATAAGGGAG
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 24
------------------------------gtgcgtttggttgctttatgttttataatatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
|| | || | |||| | || | ||||| | | || | | || ||||| || ||||||| || ||||| |||||| | || ||||| || ||| ||||||| ||||| || |||||||||||||| ||||| |||||||| |||||||||||||
tatccttcgattatctacttttgtttcatcttgtggatgatacttttacatctttggaacattttgagtgaaatcctggtttgtaat---tttgttgatgcagTTGGCTCTAAAGGCAAGTCAACTGCTGGAACAAACTAAATTAAGTGAACTTCGATCCAACATTGCTAGAAGTCTTTCTGAGTTAGAGATGTTTACAGAGG
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 24
--------------------------------------------------------------------------------------------------------------------gtgcgtttggttgctttatgttttataatatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
|| | || | |||| | || | ||||| | | || | | | || ||| || ||||||| || ||||| |||||| | || ||||| || ||| ||||||| ||||| || |||||||||||||| ||||| || ||||| ||||| |||||||
gttggacattaccctgagaaattgagttccaagttatattttttggacataccatttcttctactgggagagcattgtgaatatatatccttcaattatctacttttggtttcatcttgtggatgatacttttacatctttggaacattttgagtgaaatcctgatttaaaattttcttg---atgcagTTGGCTCTAAAGGCAAGTCAACTGCTGGAACAAACTAAATTAAGTGAACTTCGATCCAACATTGCTAGAAGTCTTTCCGAATTAGAGATGTTCACAGAGG
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 25
--------------------------gtgcgttt--ggttgct-ttatgttttata---atatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
| | ||| |||| | | ||| |||||| |||| ||| | | |||||| || | || | | | | || ||||||| || ||||| |||||| |||| ||||| |||||||| ||||| |||||||| | |||||| ||||||||||| || ||||| |||||||| || |
ttattccttgcaagttaccatcgactatccttttcaagttgatgtcatgatttatatatatatatttttaaatgttctcaa--aacg--cactatat-tttgcagTTGGCACTAAAGGCAAGTCAACTACTGGAACAAACCAAACTGAGTGAACTTCGTTCCAGCATTGCAAGAAGCCTTTCTGAATTAGAGATGTTTACTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttataatatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
aactaat putative branch site (score: 2)
tataatatttttgtct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtttggttgctttatgttttataatatttttgtctacactctcaactaatgatcagtttgtgtgtgtagTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC