Sequence
atgc intronic sequence ATGC exonic sequence...gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 1
-gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG
||| ||| || || | | | | | | | | || | | | | || | || || | ||| | ||||||||||||| || ||||||||||| ||| || |||| ||| || || | ||||| ||||||||||| ||||||||||| ||| | ||||||
tgttcatctgattggtgttctattcttggtgctacatggcatggtgatgtttgaacaaggatgtgttgaatagtgacccgttgcttgt-tatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 1
-gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG
|||| ||| || || | | | | | | | || | | | | || | | || || | || | ||||||||||||| || ||||||||||| ||| || |||| ||| || || | ||||| ||||||||||| ||||||||||| ||| | |||||||
tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgt-tattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G12350.2 (Glycine max), 3'ss of exon 1
-gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG-
|||| ||| || || | | | | | | | || | | | | || | | || || | || | ||||||||||||| || ||||||||||| ||| || |||| ||| || || | ||||| ||||||||||| ||||||||||| ||| | |||||||
tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgt-tattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG
aactaat putative branch site (score: 2)
tctttgtt putative PPT
taatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -agtagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacgaa