Sequence
atgc intronic sequence ATGC exonic sequencegtatatacttttaaatcttccattatgtactatcctaaaacaaaacatgaaatatattcatagattaactaattatcctgcagAATTTCATTGATCTTGCTGGAAGTGAACGTGCATCTCAATCATTATCAGCTGGCACAAGGTTGAAAGAAGGTGGTCATATAAACCGAAGTTTACTAACAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51150.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 7
-------------gtatatacttttaaatcttccattatgtactatcctaaaaca-aaacatgaaatatattcatagattaactaattatcc---tgcagAATTTCATTGATCTTGCTGGAAGTGAACGTGCATCTCAATCATTATCAGCTGGCACAAGGTTGAAAGAAGGTGGTCATATAAACCGAAGTTTACTAACAC
| | | || | | | | | || || || |||| || | | | | || | | || | | | ||||||||| ||||||||||||| ||||| ||| |||| ||| || |||||||| || ||||||||||| ||| | || ||||| || ||||||||||| |
gtacgactgattcactcagattacagaaaaatatagaa-gaattactctgttacttgaacaataattggaaaccaaaatgatattttttttcgggtacagAATTTCGTTGATCTTGCTGGGAGTGAGCGTTCATCCCAAACAAATTCAGCTGGTACGAGGTTGAAAGAGGGTTGCCACATAAATCGTAGTTTACTAACTC
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 7
gtatatacttttaaatcttcca--ttatgtactatcctaaaacaa---------aacatgaaatatattcatagattaa-------ctaattatcc---tgcagAATTTCATTGATCTTGCTGGAAGTGAACGTGCATCTCAATCATTATCAGCTGGCACAAGGTTGAAAGAAGGTGGTCATATAAACCGAAGTTTACTAACAC
|||| | | || || ||| | | ||||| || || |||| ||| | | | || | || ||| | ||||||||| ||||||||||||| ||||| || ||||| ||| | |||||||| || ||||||||||| ||| | || ||||| || ||||||||||| |
----gtactactgagtcactcagattacagaaaaatataaaagaattactctgttacttgaacaataattggaaaccaaaatgatattttttttccgggtacagAATTTCGTTGATCTTGCTGGGAGTGAGCGCGCATCCCAAACTAATTCAGCTGGTACGAGGTTGAAAGAGGGTTGCCACATAAATCGTAGTTTACTAACTC
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 7
------------------gtatatacttttaaatcttccattatgtactatcctaaaacaaaacatgaaatatattcatagattaac-----taattatcctgc------agAATTTCATTGATCTTGCTGGAAGTGAACGTGCATCTCAATCATTATCAGCTGGCACAAGGTTGAAAGAAGGTGGTCATATAAACCGAAGTTTACTAACAC
|||| || || || | | || | | ||||||| |||| | || | || | || | | ||||| ||||||| ||||||||||||||||||| ||||||||||| ||||||||||||||||||||| ||||||||||| | || |||||||| |||||| |||| |
gtatggatcattaatttattatagaccaatagttcagctaatacttgcagaaaacaaacaaataatgataggcatatagcaatcctcactcttattaaccctgcctgtatagAATTTTGTTGATCTTGCTGGAAGTGAGCGTGCATCTCAGTCATTATCAGCTGGCACAAGGCTGAAAGAAGGTTGCCACATAAACCGCAGTTTATTAACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actatcctaaaacaaaacatgaaatatattcatagattaactaattatcctgcagAATTTCATTGATCTTGCTGGAAGTGAACGTGCATCTCAATCATTATCAGCTGGCACAAGGTTGAAAGAAGGTGGTCATATAAACCGAAGTTTACTAACAC
aactaat putative branch site (score: 2)
ttatcct CT-rich tract
aaaacatgaaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatacttttaaatcttccattatgtactatcctaaaacaaaacatgaaatatattcatagattaactaattatcctgcagAATTTCATTGATCTTGCTGGAAGTGAACGTGCATCTCAATCATTATCAGCTGGCACAAGGTTGAAAGAAGGTGGTCATATAAACCGAAGTTTACTAACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG