Sequence
atgc intronic sequence ATGC exonic sequencegtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16950.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
------------------gtcggttttatttgcatata-cataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
| | |||| | | | ||| ||||| | | | | | |||| | | ||||| || |||| ||||||||||||| || |||||||| ||||||||||||||| | |||||||| ||||| |||||||| || ||||| ||||
gtatgttgaaacaaatgaattaccatgctttgttcagaataatcctcttcctggcttgtatgggatctaacatgcca--tgcatttttatttgt---agGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
---------------------------gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| |||| || || | ||| |||| | ||| || ||| || ||||| | || ||| ||| ||||||| || ||||| || ||||| ||||||||||| ||| | ||||| || ||||| |||||||| |||||||| || |
gtggcacattctagttgcatgttgggtttcacttttcattagtta-agatatctttggatcatcatcacttcctttgatatga-acatatattactat-----gcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
gtcggtttta--tttgcatatacataccttttccttg--tcagcaattctttctatat----gctaaattcatttctac--ttgtgat--agGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| ||| | ||| | || | ||||||| || | | || | || || |||||| | || || | || |||| || || || || |||||||| ||||||||||| || | |||||||| ||||| |||||||| ||||||||||| |
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
----------------gtcggttttatttgcatatacataccttttcc----ttgtcagcaattctttcta-tatgctaaattcatttctacttgtg-atagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| ||| || | | | ||||| | | || ||| ||| ||| | | ||||| || | | || || ||||||| || || || || || || |||||||||||||| | |||||||| ||||||||||| || |||||||| || |
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| |||| || | ||| || ||||| | ||| | | | | | || | || | | ||||||||||| | ||||| |||||||||||| | ||||| || |||||||||| ||||| |||||||| ||||||||||| |
gtttgtttcatgaatacata-attttttttcttggtctgacacattgt-----tactgatttagagtatgga-atgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| || | | | | | | || ||| | | | | || || || | | || | | |||||||| || | || ||||| ||||||||||| ||||| || |||||||||| ||||| |||||||| ||||||||||| |
gtttgtctcaacttctcaagtaataattatccctccctg-acttattgttactgacatagg--atgtgga---atgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| || | | || | || || || ||| | | | | || || || | | || | | |||||||| || | || || || ||||||||||| ||||| || |||||||||| ||||| |||||||| ||||||||||| |
gtttgtctcaatttctcatgcaataattatccctccctg-acttattgttactgacatagg--atgtgga---atgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
gtcggttttat---ttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| |||| | || ||| ||| | ||| || || | | | | |||| | || | | ||||||||||| | ||||| || ||||||||||| ||||| || |||||||||| ||||| ||||| || ||||||||||| |
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgt-tgctgatttagagtatgga-atgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------gtcggttttatttgcatatacataccttttccttgtcagca-attctttctatatgctaaattcatttctact-----tgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
|| | ||| || || | | | | | || | || ||| || || | | | | ||| ||||| ||| | ||||||||||| |||||||| ||||| || |||||||||| |||||||| || |||||||| |||||||
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------gtcggttttatttgcatataca---taccttttccttgtcagcaa--ttctttctatatgctaaattcatttctacttgtgata--gGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
| | || || | || | | | | || || || || | || | || || |||||| ||||||||| | || || |||||||| |||||||| ||| ||||| | ||||||||||| ||||||||||| || ||||
cattagtaattctaactctactagatgactgaacggggcagttggtgtctaccaagaaagttattaaaacctgtctgcctgtgttgtaacggtgatacagGTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
tgctaaa putative branch site (score: 2)
tttctactt putative PPT
aattctttctatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA