Sequence
atgc intronic sequence ATGC exonic sequence...cgaaaaaggttgaaatctttgatcattaaacaaaaaatgggtttagtgattctaaactagaaaaagactatgtttttggttccataatttggatttgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 2
cgaaaaaggttgaaatctttgatcattaaacaaaaaatgg-gtttagtgattctaaactagaaaaagactatgtt---tttggttccataatttggatttgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
|| | | || ||||| | |||| || | | | | | | | | | ||| ||||| | | ||||| ||||| || |||| ||| |||||||||||||| || ||||| || |||||||| || ||| | || |||||| |||| || ||| |||| || |||||||| |||
tgagtttctgtatgtttttctttcattttgtagaaaagggcatctgataaatttgattttttttttttgtgtgtgtgatttgggttcttaattga----tgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0020g03380.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------cgaaaaagg-------ttgaaatctttgatcattaaacaaaaaatgggtttagtgattctaaactagaaaaagactatgtttttggttccataatttggatttgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
||| || ||| ||| | | || || | || | ||| | | || | | ||||| | | |||| ||||||| ||||||| || ||||||||| |||| || |||||||| |||||||| || ||||| | |||||| ||||||||||| ||||||| |||||||| |||
gtatgagacttttctgcataaccttctcaaatttttgaagaatcctctcttttggaattctgtggctttttttgaatgg-gtattctctagctctccatttaaagggttgtctttttttcttcctgtaatg-atttttgcagATACAGAGCCTTCGATGAGTATGAAGGGATTGAAGTAGCCTGGAACCAGGTGAAGCTTAATGATTTCCTGCAGAGTCCTGAAGAGCTGGAGAGGCTGTAC
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0030g01660.t01 (Vitis vinifera), 3'ss of exon 2
cgaaaaaggttgaaatctttgatcattaaacaaaaaatgggtttagtgattctaaactagaaaaa-gactatgtttttggttccataatttggatt--tgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
||| |||| | | || || || || | | | || | | | || || | | ||| || || | ||| ||||||||||||| ||| ||||||||| |||| || ||||| || |||||||| || ||||| || |||||| |||| || ||| |||| || ||||||||||||
---caaaatttgagctttgtgggtcttcaaaaagactttttccaaatgggtttttggtggatttgtgattgactggttgtttttttatgcttgatcggtgcagTTACAGAGCATTCGATGAGTATGAAGGCATTGAAGTTGCTTGGAACCAGGTCAAGCTTTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgattctaaactagaaaaagactatgtttttggttccataatttggatttgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
ttctaaa putative branch site (score: 2)
tatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgaaaaaggttgaaatctttgatcattaaacaaaaaatgggtttagtgattctaaactagaaaaagactatgtttttggttccataatttggatttgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-gaaaaag
- - - - - tgaaatc
- - - - - - - - - - - -cattaaa
- - - - - - - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - - -ggtttag
- - - - - - - - - - - - - - - - - - - - - - - - - -ctaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa