Sequence
atgc intronic sequence ATGC exonic sequence...gaagaagacagtttatggttacatacatacataaaaactgaactttttcaatgttggaaacagccacagtacagttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G17440.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 6
--gaagaagacagtttatggttacatacatacataaaaactgaactttttcaatgttggaaacagccaca-gtacagttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
| | | || || ||| | || | | ||||| |||| ||| | | || | || | | | ||| || |||||||||||||||||| |||||||| ||||||| | ||||| || || ||| | || |||
gagtgggatggagggagcatttgcattggt-tatggtgctagtagttttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgtt--agGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 6
gaagaagacagtttatggttacatacatacataaaaactgaactttttcaa-tgttggaaacagccacagtacagt--tatgatatctgtacgttt---atttc---agGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
||| | | | | | || | || | || ||| | || || ||| ||| ||| | | | || |||| ||| |||||||| |||||||||||||| |||||||| | |||||||| |||||||| || |||
---------gatttctagacttcctctagaacataagcaagttttctgtaactgtataggattgctcttatatagtgttattgtattttaatggttgtcattttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
gaagaagacagtttatggttacatacatacataaaaactga--actttttcaatgttggaaaca-gccacagtacag--ttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
| | | | | | | | |||| || || | ||| ||| || | | ||| | || | || ||| ||||| | |||||||||||| |||||||||||||| || ||||| | |||||||| |||||||| || |||
---tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgt-cgttt-tggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G47910.1 (Glycine max), 3'ss of exon 6
gaagaagacagttta-tggttacatacatacataaa-aactgaactttttcaatgttggaaacagccacagtacagttatgatatctgtacgtttatt--tcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
|| |||| || | || ||| |||| |||| | ||| || | | | | ||||||| | | || | | ||||||| ||||| ||||||||||| || || |||||||| |||||||| ||||| |||||||||
----aatgtgttttaatgtcaatatcgatatataattgactgctgcatggtaatcatgactcttgatagcattttttaatgatatgtattttttgaataaacagGTGAGCAAGGAATGGTTGATGAGGCTCAAAAAGCACTGGAAGAGGCTGAAGCACTTAAGAAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 6
gaagaagacagtttatggttacatacatacataaaaactgaactttttcaatgttggaaacagccacagtacagtta-tgatatctgtacgtttatt--tcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
| | | | | || ||| || |||| || | | ||| |||||| | | || | | ||||||| ||||| ||||||||||| || || |||||| | |||||||| ||||| |||||||||
---cttaatgataagcaaatttcaagagccacaaactttgtcctttgcgttctcctaggctctttactttttatttaatgatatgtattttttgaatgaacagGTGAGCAAGGAATGGTTGATGAGGCTCAAAAAGCATTGGAAGAGGCTGAAGCACTTAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaatgttggaaacagccacagtacagttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
tttatttc CT-rich tract
ttatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagaagacagtttatggttacatacatacataaaaactgaactttttcaatgttggaaacagccacagtacagttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- -gaagaca
- - - - - - - - - - acataca
- - - - - - - - - - - - - - - -taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacag