Sequence
atgc intronic sequence ATGC exonic sequencegtgagtattttctttttacttactctttgattactaaggcttgtttcattgagattaatttctggtttatattcttagGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 7
-------------gtgagtattttctttttacttac--tctttgattactaaggcttgtttcattga--gattaatttctggtttatattcttagGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
| | |||| |||| | |||| || || | || |||| | ||| | || | | | | |||||||||| || |||||||||| |||||||| ||||| |||| || ||||||||||||||||| ||||| || || | || || | || || || |||
gtaagttgtttctctttcaggtctcttcctactggcagtcttagaaggtatagtgattttccattagctcactaaataatgatgtgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 7
gtgagtattttcttttta---------cttact-----ctttgattactaaggcttgtttcattgag--attaatttctggtttatattctt-agGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
|||||| ||||| ||| | |||| || | | | | || | || | ||| | || | ||| ||||| |||||||| || |||||||||| |||||||| ||||| |||| || ||||||||||||||||| ||||| || || | || || | || || || |||
gtgagttgtttctctttcaggtctcttcctactagcagtcttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtgagtattttctttttacttactctttgattactaaggcttgtttcattgagattaatttctg------gtttatattcttagGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
|| | | || | | | ||| | | || | | |||| | || || || || | ||| | |||||||||| || |||||||| | |||||||||||||| |||| || || |||||||||||||| ||||| || | | || || | || || || |||
gtaagtaataattctgttttataatattttattttaatatatatagtaactcttct-tctacactaagttcaaagatattccaattattttcctctagttttcttgatgacaaggatgtatctctttagGTTTCCTGTTGATGAGAATTCAACTATGAAGTCAGTAGTTGAATACTTTCAAGAGATGTATGGTTTCACAATTAAATATACTCACCTTCCTTGCCTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgattactaaggcttgtttcattgagattaatttctggtttatattcttagGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
gattaat putative branch site (score: 3)
tattctt putative PPT
attgagattaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtattttctttttacttactctttgattactaaggcttgtttcattgagattaatttctggtttatattcttagGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG