Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttagttacgaaattagagttctttcggattccaatatactttgattttgcttttatttgattgtgatatgttgcttttgtttgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtgagttttagttacgaaattagagttctttcggattccaatatactttgattttgcttttatttgattgtgatatgttgcttttgtttgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG
| | | | || || ||| ||| | | || | | ||| | |||| | ||| || || | ||||||| || ||||| ||||||||| |||| ||||| | ||||||||||||| || |||||||| || || ||||| ||||| |||||||| |||||||||||||||||||
gtgagtaccctcaagttttgaatttcacgatttctgaaactgttcgaacgaaaatcagaagaaaaaaaattgggttgaaattggtttctcaaattgcgggggggatgggaataaaaagctagggttttgttaga----gaagggttgaagatttatcatgattttaac-tgaagtgctgtgtgtgtttgtggtga------tagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------gtgagttttagttacgaaattagagttctttcggattccaatatactttgattttgcttttatttgattgtgatatgttgcttttgtttgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG
| | | | | | || |||| ||| | | | | |||| || | ||| | || | | || | |||||||| |||| | |||| |||||||| |||| | ||| | ||||||||||||| || |||||||| || || ||||| ||||| ||||| || |||||||||||||||||||
gtgaggactctcaattgaatctcaggattctgaaattgttcgaaaatcaaaggaaaaaaaatagggttgatatttgtttctgaaactgtgggggaatgaaataagaaagttagggtttagtttattatggagaagagttgaagtttgatggttttaactgaactgttgtgtgtgtgtttgtttgtggtgct--agTTCGATGGGTTCTTGAAAGACGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACAACTCTTGCTTTTATATTTAAAGAGGGTGTTATGGTAGCTGCTG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtgagttttagttacgaaattagagttctttcggattccaatatactttgat-tttgcttttatttga--ttgtgatatgttgcttttgtt--tgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG
| | | || || | | || || ||| | | | | || | |||| | || || || || | || |||| | ||||| |||||||||||||||||||| | ||| | | ||||||||||| |||||||| ||||| || ||||| || || |||||||| ||||| ||||| |||||||
gtgagttctgatacatttgatttagaatcttcctatcaatgaaaaaaaggctcaatttggaatgtgatgtcacactttcctttagtagaaattagaatcagtagggactgaaaatgttttccctttttcagTTTGATGGGTTTCAGAAAGATGCTATTCAAATGGTGAAGCCAGCAAAGGGAACAACAACTCTTGCCTTCATTTTTAAGGAGGGTGTAATGGTTGCTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgcttttatttgattgtgatatgttgcttttgtttgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG
atttgat putative branch site (score: 5)
tttttt putative PPT
ttttatttgattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttttagttacgaaattagagttctttcggattccaatatactttgattttgcttttatttgattgtgatatgttgcttttgtttgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT