Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacgttatcttagtagacaaatgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65510.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 8
-----------------------gtaaaacgttatcttagtagacaaatgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
|| | ||| || | | || | ||||| |||| | | | | || | ||| | ||||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||||| || ||||| | ||
tggcttgacttgaaacagtgattttacattgtttgtcatttatatgaggtggaaatagaatattctgaataatcatctaactca---gttcacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATAAAGTTCAGAGGTGCAAACGCGGTAACCAACTTTGAGATGAATAGATATGATGTGGA
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 8
------------------------gtaaaacgttatct-tagtagacaaatgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
| | | || | || || | | || | || |||| |||| | | | | | | | ||| | ||||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||| || ||||| | ||
tttgacttgaaacagttagtttacattagttatcatttatatgaggtggaaatagaatattcca---tgaataatcatctaactcagt--tccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 6
------------gtaaaacgttatcttagt-agaca------aatgtcctattcttcaccctgaaaaatccagtca---ttgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
| || | || ||||| | | | ||||| || | | | || | | | ||| ||| | || ||| | |||||| |||||||| ||||||||||||||||||||||||||||||||||||||||| | ||| ||||| || || ||||||| | |||||| | ||
gacttgaaagttgaaacaagtcttcttacttacattttctataatgtttgttttattattatttgaacttgaagaaattttggttcttgcat-tgttt-cagCAACTGAAGAGGAGGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGTTCGAGCGCCGTAACCAATTTCGAGATGAGTCGATATGACGTCGA
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G29400.1 (Glycine max), 3'ss of exon 4
----------------------------------------gtaaaacgtta--tcttagtagacaaatgtcctattcttcaccctgaaaaatccagtca---ttgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
|| | | | | | | | | |||| || | || || | ||| ||| | || ||| || |||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| | || ||||| || ||
tgatagcatgtcttgaaagttaaaacaatttttcttacatgttagataatggttaccattttgtttgttttttattttttattcttttgaacttgaatagTTTTGGTTCATGCAT-TGT-TACAGCAACTGAAGAGGAGGCAGCAGAGGCATATGATATTGCAGCCATAAAGTTCAGAGGTGCAAGTGCCGTAACCAATTTC-----------------------
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtaaaacgttatcttagtagacaaatgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
|| | ||||| ||| | || | | | | | || || | || ||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| || | || || || || || || ||||||||| | ||||| | ||
ggtcactggacgtgctaaaattaggctaatgtcttaaaagaggggtctcaaaaagaagcatattgttcacataataatcccttgtaactcgtggtgtcagCCACCGAAGAGGAAGCAGCAGAGGCATATGACATAGCAGCCATAAAGTTCAGGGGTGTGAATGCGGTGACCAATTTCGAGATGAACCGATATGATGTGGA
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0772g00020.t01 (Vitis vinifera), 3'ss of exon 6
----gtaaaacgttatcttagtagacaaatgtcctatt-------cttcaccctgaaaaatccagtc-----attgattc---gtatatatgtgtat-agCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
|||| | | | ||| | |||||| || ||| ||| || || | | || | ||| | |||| ||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| || | || || || || || || ||||||||| | ||||| | ||
ggtcactggacgtgctataattaggctaatgtcttaaaagaggggtctcaaaaagaagcatattgttcacataataatcccttgtaactcgtggtatcagCCACCGAAGAGGAAGCAGCAGAGGCATATGACATAGCAGCCATAAAGTTCAGGGGTGTGAATGCGGTGACCAATTTCGAGATGAACCGATATGATGTGGA
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------------------gtaaaacgttatcttagtagacaaatgtcctat--tcttcaccctgaaaaatccagtcattgattcgtatatatgtgtat-agCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
| |||| | | | || || | | || | ||| | ||| | | | | || | || || ||||||||||||||||||| || |||||||| || ||||| ||| | |||||||| || || || ||||| || ||| | || | ||
gtgagtgccggtttcacatgaatttgtaaacattagtggattaccctcgctgcaaatcctggtcgtttctcctgataggacttctgatatcgattccggagacatcagcatattctgggtctcgttgcaatgttgaaaggatttcgcagggtgcccatgttacctaatggttaaaatgaactggctttgtatgactcagGCACACAAGAGGAAGCAGCAGAGGCCTACGACATTGCCGCGATAAAATTCCGTGGAATCAATGCCGTCACAAACTTCGACATGTCTCGTTACAATGCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
cattgat putative branch site (score: 4)
tatatatgtgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacgttatcttagtagacaaatgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG