Sequence
atgc intronic sequence ATGC exonic sequencegtatttattgacccttaattctaaaatttctcttcggtggagtaagatttcccgttgtttgattcgcgataactgtctattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G62640.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G62640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G44350.1 (Glycine max), 3'ss of exon 3
gtatttattgaccctta--attctaaaatttctcttcggtggagtaagat-ttcccgttgtttgattcgcgataactgtctattgatg---------gcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA-
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--gattatagcttattattgtattcatatctctccaagattgagcgtcttcttttcatttctggaacctctcctataatttattgtcattacaacatgcagaTTCAAAAACAACTTGGCTGCAAAGCAAATCCATTGTCTTATGACATTACAGCTGCATGTAGTGGATTTGTGTTGGGTTTAATATCAGCTGCTTGTCACAT
upper sequence: AT1G62640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 3
--------gtatttattg-acccttaattct--aaaatt---tctcttcggtggagtaagatttcccgttgtttgattcgcgataactgtc--tattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
| |||||| | || || ||| || ||| | ||||| | | | | || |||| | || || | |||| || |||||||||||| ||||| |||| || || |||||| ||||||| || |||||||| |||||||||||||| |||||| || | ||||||||||| || |
gattatagcttattattgtatccatagctctccaagattgggtgtcttcttttcatttatggaacctcttgtataat-----attattgtcattacaacatgcagATTCAAAAACAGCTTGGCTGCAAAACAAATCCATTGTCTTATGACATTACAGCTGCATGTAGTGGATTTGTGTTGGGTTTAATATCAGCTGCTTGCCACA
upper sequence: AT1G62640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G00550.1 (Glycine max), 3'ss of exon 2
----gtatttattgacccttaattctaaaatttctcttcggtggagtaagatttcccgttgtttgattcgcgataactgtctattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
||| | || || | |||||| | | ||| | | ||||| || || ||| | | || | || | |||||||| || |||||| |||| ||| || |||||| ||||||| || |||||||| |||||||||||| | ||||| || | ||| || ||||||| |
gtatgtacatcttcacaat-aattctctggctaccctttgcta-agtaatcttcttttttatttc-tgtatcctctct-tatacaacttgcagATTCCAATACAACTTGGCTGCAAAAAAAATCCATTGTCTTATGACATTACAGCTGCATGTAGTGGATTTCTGCTGGGTTTAATATCATCTTCTTGTCACA
upper sequence: AT1G62640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0154g00140.t01 (Vitis vinifera), 3'ss of exon 3
---------gtatttattgacccttaattctaaaatttctcttcggtggagtaagatttcccgttgt--ttgattcgcgataactgtctattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
|| | || | | | | | || | ||| | | | | || | | | || | | || ||||| ||||| |||||||| |||| ||| || || |||||||||||||| |||||||| ||||| |||||||| ||||||||||| ||||||||||||||||
tcaaaactctaatgttttccacttcagcttccatcttcttattctaaccattcgagtgcctttttatgctcatgttcttatgttttgtttcatatatcagATCCAAAAAGCACTTGGCTGCAAAAAAAATCCTTTGGCTTATGATATTACAGCTGCATGTAGCGGATTTGTGTTGGGTCTAGTCTCAGCTGCTTGTCATA
upper sequence: AT1G62640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0233g00060.t01 (Vitis vinifera), 3'ss of exon 3
---------gtatttattgacccttaattctaaaatttctcttcggtggagtaagatttcccgttgt--ttgattcgcgataactgtctattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
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tcaaaactctaatgttttccacttcagcttccattttcttattctaaccattcgagtgcctttttatgctcatgttcttatgttttgtttcatacatcagATCCAAAAAGCACTTGGCTGCAAAAAAAATCCTTTGGCTTACGATATTACAGCTGCATGTAGCGGATTTGTGTTGGGTCTAGTCTCAGCTGCTTGTCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggtggagtaagatttcccgttgtttgattcgcgataactgtctattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
tattgat putative branch site (score: 3)
taagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttattgacccttaattctaaaatttctcttcggtggagtaagatttcccgttgtttgattcgcgataactgtctattgatggcagATTCAAAAGGCACTTGGTTGCACAAAGAACCCATTGGCTTATGATATCACAGCTGCTTGTAGTGGATTTGTTTTGGGTCTAGTTTCAGCTGCTTGTCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT