Sequence
atgc intronic sequence ATGC exonic sequence...tgttagtatacatagctttggttagttcactttgttttgtagaacaccttccataactctgcttatttgtaatgggttttgtttttttgtctgtggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G49050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G37820.1 (Glycine max), 3'ss of exon 2
tgttagtatacatagctttggttagttcactttgttttgtag----aacaccttcca---taactctgct-tatttgtaatg-ggttttgtttttttgtctgtggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
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-------agctacggttgtgattagttgaggtcaacaggtaatggaaatgattgtcacagtaattttaatgtttttatggtaagatatttttttcttggttttg--cagTTTGCCATGCTTATTGTGCTTGAGGTGCATGAAGGATACATGCATACCAGAGGAGAAGATGCTGAAAGATCCAAGGAGACTCTATGCTCCCGGTCGCCTT
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G25180.1 (Glycine max), 3'ss of exon 3
----tgttagtatac-atagctttggttagttca-ctttgttttgtagaacaccttccataactctgcttatttgtaatgggttttgtttttttgtctgtggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
| | | | ||| | | ||||| | | | ||||| | || | | | ||||||| | || ||||| ||| ||| |||||||||||| | | ||| | |||||||||| |||||||||| |||||||| | |||||||| |||||||| || | || ||||| ||||||||| |
atgctataaaaaggtgataccaacgattagtgaaaccattatttgtgtta----ttttaatgtgttcataatttgtacttatactt-tttttctgtggctgg-cagTTTGCCATGCCTATTGTGCTTGAGGTGCATGAGGGATACATGTATTCCAGAGGAGAAGATGCTGAAAGATCCAAGGAGACTCTATGCACCTGGTCGCCTT
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G30140.1 (Glycine max), 3'ss of exon 3
-----tgttagtatacatagctt-tggttagttcactttgt-tttgtagaacaccttccataactctgcttatttgtaatgggttttgtttttttgtctg-tggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
||| | | | ||| ||||| | | ||||| || || ||| || | || | | || |||||||||| | || | |||||||||||| | | ||| | |||||||||| |||||||||| |||||||| | |||||||||| |||||| || | || ||||| || |||||| |
catactgtaaaaaagggttgctaacaattagtgaaaccaatatttgtgtaat---tttcatg----tgttcatgt-tgatataatttgttttttgctgtggctggcagTTTGCCATGCCTATTGTGCTTGAGGTGCATGAGGGATACATGTATTCCAGAGGAGAAGATGCTCAGAGATCCCAGGAGACTCTATGCACCCGGTCGCCTT
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0050g00620.t01 (Vitis vinifera), 3'ss of exon 2
tgttagtatacatagctttggt-tagttcactttgttttgtagaacaccttccataactctgcttatttgtaatgggtt--ttgtttttttgtctgtggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
|| || | | || | ||| ||| |||| | ||||| || | || | | || | ||| |||| | | || ||||||||||||| || ||||| |||| |||||||| |||||||| || || || | |||||| ||| |||||| || |||| ||||| ||||||||| |
---ggctactcaaaacactgaagtggttggttttcttttattgaacagTTTGCCATGCTTATTATGCAAACACTGAAGTGGTTGGTTTTCTTTTATTGAACAGTTTGCCATGCTTATTATGCCTAAGATGCATGAAAGATACATGCGTCCCTGAAGAGAAGATGTTCAGAGATCCAAGGAGGCTGTATGCACCTGGTCGCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttccataactctgcttatttgtaatgggttttgtttttttgtctgtggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
ccataac putative branch site (score: 3)
ttttgtttttttgtct putative PPT
ttttgtttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttagtatacatagctttggttagttcactttgttttgtagaacaccttccataactctgcttatttgtaatgggttttgtttttttgtctgtggacagTTTGCCATGTTTGCTATGCATAAGGTGCATGAAGGATACATGTGTTCCAGAGCAAAAGATGCTCAAAGATCCTAGACGGCTTTATGCTCCTGGTCGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - gctttgg
- - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - -gaacacc
- - - - - - - - - - - - - - - - - - - - - - - - - ccataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctta