Sequence
atgc intronic sequence ATGC exonic sequencegtaagaccctcttaatcattatttgggtctagcattttgagctgtttgcttaacagatgtttttaccaccatgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10940.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10940.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g08830.1 (Oryza sativa), 3'ss of exon 5
-----------------------gtaagaccctcttaatcattatttgggtctagc--attttgagctgtttgcttaacagatgtttttaccaccatgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
| | | | ||| ||||| | ||| | | || | | ||| || | | ||| | | ||| |||| ||| ||||||||| ||| | || |||||||| ||||| ||||| ||| |||| ||||||||||| ||||| | | || ||||||| ||| ||
tgtgctctagtttcttgtggattgagatttctacccaattattataagcctctgcctggtcttcaattatttaattttttgtattgtttgctat-atgcagGTTGAAATTGGTAACCCTAATATAGTCTGGAGTGCAAGTGAGGATGGAACTCTAAGACAGCATGATTTTCGGGAGTGCAGTTCCTGTCCTCGTGCAAGAT
upper sequence: AT5G10940.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G09890.3 (Glycine max), 3'ss of exon 5
-----------------------gtaagaccctcttaatcattatttgggtctagcattttgagctgtttgcttaacagatgtttttaccaccatgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
|||||| || || || ||| |||| || | |||| | | | | || | || |||| ||| ||| ||||||||||| |||||||||||||||||||||||||| ||||||| |||||||| |||||| ||||||||||||||| ||||||
gtaagtcatgtggtctctaagaaataagacagaatttat-atgggaaaaatct-gcatcatgtga-gttttcatgtcttccctgttc-cttttttgcagGTTGAAAATGGAAACCCCAATGTAGTATGGAGTGCTAGTGAAGATGGGACCCTAAGGCAACATGATTTTCGGGAAGGTACCTCTTGTCCTCCAGCTGGAT
upper sequence: AT5G10940.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G09930.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------gtaagaccctcttaatcattatttgggtct-agcattttgagctgtttgcttaacagatgtttt------taccaccatgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
| | | | || ||| || || | | | || | || | |||| || | | || |||| ||| ||| ||||||||||| ||||||||||||||||||||||||||| ||||||| |||||||| |||||| |||||||||||||| ||||||
gtaagttatgaagaatatactaatttaacataatttcaataacttcacatcaatgggattaaaggaaataaaacataatccatgtgggaaaaatctgcatcatgtgagtttttcatgtcttccatggtccttttttgcagGTTGAAAATGGAAACCCCAATGTAGTATGGAGTGCTAGTGAAGATGGGACTCTAAGGCAACATGATTTTCGGGAAGGCACCTCTTGTCCTCCAGCTGGAT
upper sequence: AT5G10940.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g07170.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------gtaagaccctcttaatcattatttgggtctagcattttgagct--gtttgcttaacagatgtttttaccacca-tgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
| | || | || | || | || | || | | | ||||| || | | | || |||| ||| ||| ||||| ||||| ||||||||||| ||||||||||| || || ||||||||||| || ||||| | | || ||||| || |||||
gtaagatctcatcacaggccatacagttctttagaggtcaactatttaaatgaagttgtatgagtatgggaactggaaatccaggtatttcatgatggtatttggcagcttgaatatcaaagttcacctgcttgcttttgcttctcatacttactgcagGTGGAAGTTGGAAACCCTAATGTGGTATGGAGTGCAAGTGAAGATGGAACCTTGAGGCAGCATGACTTTCGGGAGGGTGCTTCCTGTCCCCCAGCTGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgggtctagcattttgagctgtttgcttaacagatgtttttaccaccatgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
gcttaac putative branch site (score: 3)
tttttacc putative PPT
atgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaccctcttaatcattatttgggtctagcattttgagctgtttgcttaacagatgtttttaccaccatgtagGTCGAACCTGGTAACCCCAATGTTGTATGGAGTGCTAGTGAAGATGGGACTTTAAGGCAGCATGATTTCCGGGAATCTACCTCTTGTCCTCCTGCTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA