Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaaccctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25840.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25840.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G20810.1 (Glycine max), 3'ss of exon 7
gtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaacc-ctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
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---------------------------------------------------------------------------------tttttatgacat-acagttgtcaatctactgtttatttagt--ttggggt---tttattgtaggtttgt----tttcttggtatcttaagatttccttccttctttgaagG--GTAAAGGAGAAGGTTTACGGATTGAGAGGGGTGGCCTTCACGACAATTGGGATGATGCAGAGGGTTATTACA
upper sequence: AT3G25840.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24820.1 (Glycine max), 3'ss of exon 7
gtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaaccctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
| | ||| || | || | | || | |||||| || | | | | | || ||| || || || | | | || || |||||||| || | ||||| |||||| | | || | |||| || || ||||| |||||||| |||||||||||||||||||
---------------------------------------------------------------------------tgtcaagcttgcctttagggtaat----aggtgatttttcgttcatttatttatttattcttatga---cttatattaactattaagattttctac--------cttcttttcagG--GAAAAGGAGATGGTTTGCTGATTGAGAGGGTTGGCCTACATGACAATTGGGACGATGCAGAGGGTTATTATA
upper sequence: AT3G25840.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 10
gtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaaccctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
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------------------------------------------------------------------------------------------cctctctgtcaagcttgccttttagggtaatagttgatttttcgtttatttatttatttgctcttagattaactattaagatttcctaccttcttttcagG--GAAAAGGAGATGGTTTACTGATTGAGAGGGCTGGCCTACATGACAATTGGGACGATGCAGAGGGTTATTATA
upper sequence: AT3G25840.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaaccctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
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----------------------------------------------------------------------tgtcctattta--ttaatgccttga-----gtga---cctttgtttgtgat-tttggaactaatatctta-----tttcaatcatgcttgacctg----attggtattttttcttttcagG--GAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
ttttaat putative branch site (score: 3)
cccacttctttt putative PPT
tttttaatattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaaccctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG