Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaccctaatgaatcttatgcaattattatctttgtttggcccgaacatgacattgattctggtctacctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08450.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 4
gtatgtaccctaatgaatcttatgcaattattatctttgtttggcccgaacatgac---------attgattctggtcta-----cctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
|||||| || | | || | || | ||| | || | | || ||| || | ||| | | ||| |||||||||||||||||||||| ||||| || ||||||||||| ||||| | | | |||||| ||||||| || ||| |||| | || | |||||||
gtatgtgttgcaaaaaggttgcagctagctttttatttctagggactggacttgatgtgtttgaaatcagtactgattttgcatttttgttgcatagTTCTCATGCATACAGGTTATTGTCGCCCAACAGCTTCTCCACCTCCCATGGCTGTACAAGAGTTGCGCACAACCATTCGAGTGCTACCTCCGCAAGATT
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 3
gtatgtaccctaatgaatcttatgcaatta--ttatctttgt-ttggcccgaacatgac---------attgattctggtctacc-----tgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
|||||| | || ||||| || || | ||| |||| | | || ||| || | ||| | | | ||| |||||||||||||||||||||| ||||| || ||||||||||| |||| | | | |||||| ||||||| || ||| ||| | || | |||||||
gtatgtgttgttgcaaaaaggttgcaactagctttttattgcattggactggacttgatgtgtttgaaatcagtactgatttttcatttttgttgcatagTTCTCATGCATACAGGTTATTGTCGCCCAACAGCTTCTCCACCTCACATGGCTGTACAAGAGTTGCGCACAACCATTCAAGTGCTACCTCCGCAAGATT
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 4
----------------------gtatgtaccctaatgaatcttatgcaattattatctttgtttggcccgaacatgacattgattctggtctacctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
| || | || | || || | ||| |||| || | ||| || | ||||| ||||||||||||||||||||||||||| || ||||| ||||| || | | | || ||||| |||| | || || | || | || | |||||||
gtatatgtctttacaaaaagatgcatttgccttttcttataaatgacaggtcatatatttggcgatagtatggataattgcaattttgttgcacctgca---cagTTCTCATGCATACAGGTTACTGTCGCCCAACAGCGTCTCCACCCCATGCAGCCATACAAGAATTGCGTGCAACCGTTCGTGTACTACCTCCTCAAGATT
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 5
----------------------gtatgtaccctaatgaatcttatgcaattattatctttgtttggcccgaacatgacattgattctggtctacctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
| || || | || || || ||| |||| || | ||| || | ||||| ||||||||||||||| ||||||||||| || ||||| ||||| |||| | | || ||||| |||| | ||| | | || | || | |||||||
gtatatgtcttcaaaaaaagatgcattagccttttcttataaatgacagttcatatatttggcgatagtatggataattgcaattttgttgcacctgca---cagTTCTCATGCATACCGGTTACTGTCGCCCAACAGCATCTCCACCTCATGCAGCCATACAAGAATTGCGTGCAACTGTCCGTGTGCTACCTCCTCAAGATT
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtatgtaccctaa--tgaatct-tatgcaattattatctttgtttggcccgaacatgacattgattctggtctacctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
|| | | | || || || | || || | || | ||| ||| | | ||| || ||| || |||| | ||||||||||||||| || || ||||| || || ||||||||||||||||| | || || ||||| || |||| || | || | || |||||||||
gtatgtggtgttacaaaggagagtctagagcttatactgcatttgtagatgatagaacttagtggtatgccataactt-atattaatgctgcattat-tgtctttcagTTCTCATGCATACGGGCTATTGTCGCCCAACGGCTTCTCCTCCTCCACCTGCTATTCAGGAGCTACGTGCTACCATCCGGGTGCTACCTCCACAAGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattatctttgtttggcccgaacatgacattgattctggtctacctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
cattgat putative branch site (score: 4)
tctacct putative PPT
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaccctaatgaatcttatgcaattattatctttgtttggcccgaacatgacattgattctggtctacctgtcatctagTTCTCATGCATACAGGTTACTGTCGTCCCACAGCTTCTCCTCCTCCACCGACAATGCAAGAGCTGCGCACTACTATTAGAGTCTTGCCGTCACAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC