Sequence
atgc intronic sequence ATGC exonic sequencegtttactactttattcaccttctgagtcgatgttatttcgcttcattgcacatgatttgtaatcttgaactgaatgttaaatttcttctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18000.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G060886_T01 (Zea mays), 3'ss of exon 4
-----------------------gtttactactttattcaccttctgagtcgatgttatttcgcttcattgcacatgatt-tgtaatc--ttgaactgaatgttaaatttcttctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
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gtattgaaatttgcaatgtcttggtataaaagttttgtg--tttgccaactgatggccttcatctgatttatagatgtttgtatggttgattcattcaattcttttatgcattttttcttgcagAATGAAAGCATTAATGGTCACTACAAGAATGCATCCTTTATGTGTGCTGATGTGACATCCCAGGACCTAGTGCTTCAAGCTAACTCCATCGATCTGATAT
upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G11580.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------gtttactacttt-attcaccttctgagtcgatgt-tatttcgcttcattgcacatgatt--tgtaat--cttgaactgaatgttaaatttct---tctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
|| || | ||| || | || | | |||| | | | || | |||| | | |||| | | || || | | | | || || |||||||||| || ||||| || |||||||||||||||| |||||||||||||| || || || || | | || |||| ||||| |||| |||| |
gtaataccaatttcttaccacactttgaacactaattaataattatgtttgtctattttttttataaaaaaattggtcccacccatattgtgatataatgta-atgactaatataatgaccttaattggtttctcatctcacataatctttctgcagAATGAAAGCATTAATGGACACCACAAGAATGTCAAGTTCATGTGTGCTGATGTCACTTCTCCAAACTTGCATATTTCTGAAGGATCAGTTGATCTGATGT
upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G30650.2 (Glycine max), 3'ss of exon 1
--------gtttactactttattc--accttctgagtcgatgttatttcgcttcattgcacatgatttgtaatcttgaactgaatgttaaatttcttctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
|| || | ||||||| ||| || | | | | | | | | || | | ||||| || | | | || | ||| || |||||||||| || ||||| || |||||||||||||||| |||||||||||||| || || || || | | || |||| ||||| |||| |||| |
aaatccttgtataattttttattcctacccgctaaaaaaaaatagtgatgtatta------acgagtaatgatctt-aatttctcatcccacatcat-tttgatgcagAATGAAAGCATTAATGGACACCACAAGAATGTCAAGTTCATGTGTGCTGATGTCACTTCTCCAAACTTGTATATTTCTGAAGGATCGGTTGATCTGATAT
upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g02430.t01 (Vitis vinifera), 3'ss of exon 3
---------gtttactactttatt---caccttctgagtcgatgttatttcgcttcattgcacatgatttgtaatcttgaactgaatgttaaatttct---tctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
|||| |||| || | | |||| | | | | | | | | | | | | ||||| || |||| || | ||| |||||||||| || |||||||| |||||||||||||||||||||||||||||||| |||| || || || || | | | | ||| | |||||||| |
gtaactttggtttcctaccttgacaaatatcatctgttcttgtaaaaaaaaacaagaataatgctcaaatatgaagcttagttgaatcttctttttcaatgtccattttgcagAATGAAAGCATAAATGGGCACTACAAGAATGTCAAGTTTATGTGTGCTGATGTAGCATCTCCAGAGCTGAATTTTTCAGCAGAATCAGTGGACTTGATAT
upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 2
gtttactactttattcaccttctgagtcgatgttatttcgcttcattgcacatgatttgtaatcttgaactgaatgttaaatttcttctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
|| ||||||| | | || | | | || | ||| | || || || ||||| | | | || | ||| ||||||| |||||||||| | ||| ||||||| ||| ||||||||||||||||| || ||| |||| | || | || ||| | ||||||||||
--gtaaatttttattctcatcctc--ccaaattcata--gacacataaaatat-atatg-aatctcatccataccatggaaact--------ttgcagAATGAGTTCCTCAATGGGCACTTCAACAATGTCACGTTCATGTGTGCTGATGTTACTTCTCCTAACCTGGATATTTCACCAGGTTCTGTGGACTTGATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgcacatgatttgtaatcttgaactgaatgttaaatttcttctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
tttcttctttcttgt CT-rich tract
aatgttaaatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttactactttattcaccttctgagtcgatgttatttcgcttcattgcacatgatttgtaatcttgaactgaatgttaaatttcttctttcttgtagAATGAAAGTATCAATGGGCATTACAAGAATGTCAAGTTTATGTGTGCTGATGTTACATCCCCTGACCTCAAGATCACTGATGGATCTCTTGACTTGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA