Sequence
atgc intronic sequence ATGC exonic sequencegttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 12
----gttggtctcctctccgtgaatttcaagttaaaacagccatga--gaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
|| ||| ||| |||| | | || | || | || | ||| || | || || |||| | | || ||||||||||||||||| || || ||||||||| | ||| | |||||| |||| ||||||||||| || ||||||| ||||| |
gtttgtcaatcttttcttta-gaatattacgtaacaatcttttgtattgatatctaagataggatgacgaaaacttaatttcagTATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGA
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
---------gttggtctcctctccg----tgaatttcaagttaaaacagccatgagaggtttaaaattaat-----tatgt----gttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
||| | ||| | | | | ||| |||| || |||| ||| | ||| | | || | ||||| | | |||||||| ||||| |||||||| |||||||||||| | ||||||||||||||||| ||||| |||||| |||| || |||||||| |
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
--------gttggtctcctctccgtga---atttcaagttaaaacagccatgagaggtttaaaattaat----------tatgtgttgtttgtt-tacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
||| | | | | | | |||| | | || |||| ||| | || | || | || ||||| | | |||||||| ||||| |||||||| |||||||| ||| | || |||||||||||||| ||||| |||||| |||| || |||||||| |
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 12
-------------gttggtctcctctccgtgaatttcaagttaaaacagc-catgagaggtttaaa-attaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
| | | | |||| ||| | | | | || | | | | | ||| | |||| |||||| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |
gtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
------gttggtctcctctccgtgaatttcaagttaa--aacagccatgagaggtttaaaat-taattatgt----gttgtttgtt----tacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
| | || | | |||||| | || | | || | | ||| || | || || || ||||| |||||| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
gttggtctcctctccgtgaatt---tcaagttaaa-acagccatgagaggtttaaaattaattatgtgtt----gtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
||| | | | ||| || | ||| || | || || | | | | ||| || | || ||| || |||| | | || ||||| || |||||||| |||||||| || || || ||||| |||||| |||| ||||||||||| | || ||||| |||||||
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116473628|gb|EG516220.1|EG516220EST: ATAGGATTGGTCNNNNNNNNGAAGTTCAAGTGTTTCGATTCTGCACTGAG TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTT
genomic: ATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcc ... ttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
aattaat putative branch site (score: 3)
tttgttt putative PPT
tttaaaattaattatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT