Sequence
atgc intronic sequence ATGC exonic sequence...attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73460.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 3
--attgaaa-tataaaggggtcataataaactaagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
||| | ||| | | || | || | || || | || | | | ||| ||| | | |||| ||| | || || ||||||||| || ||||| || || ||||| ||||| ||||| ||| | || ||||| || || || |||||||||||||| || || || |||||||| |||||||
gttctgagactattcttcaagc-tgatgtattaggactgtctgatatctttcaaatttatgtc-attacatcctataacaaatttgaagcat-ttgtttgcagGAACATTTGCTTATAGTCTGTGAGCTTCTGAAGGCAAATTTGTATGAATTTCAAAAGTTCAACAGAGAATCAGGAGGCGAGGTCTATTTCACAATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
attgaaatataaaggggtcataataaactaag-taggtttgcattattatatctctttgtggattg--tttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
|||| || || ||| | | | | || || |||| || ||| |||| |||| | | || || |||||||||||| ||||| || || ||||||||||| ||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||||| ||||| |||||||
---taaatgactcttctccaaaacaaattgctctcgagtcacagcatcatataataaagtttgttgtgtttgctgtactacttattttaaacattgtttgcagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
---attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
||| | |||| | ||||| | | | | | | | || || || | || | | ||| | ||||||||| || ||||| || || ||||||||||| ||||| ||||| || || || || ||||| |||||||||||||| ||||| ||||| ||||| |||||||
ggaatttcagagctcagggttgataattggttcttt---tccaaagcaatttgccttaaagtcacaacatttctttaccacttatttcaaatactgtttgcagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
----attgaaatataaagggg-----tcataataaactaagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
|| ||| || | | || || | ||||||| | | | | | ||| | | | | ||| || | || | || | || || | ||||||| || ||| |||| ||||||||||| ||||| ||||| |||| || || ||||||||||| |||||||||| |||||||| ||||||||||||||||
atgttttaaaacattatgaggggctatccttttaaactatgatgttgagaaatatc-tgtttactagtg-atcatctgactttact-acgccttgtac------tgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
attgaaatataaaggggtcataataaact--aagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttct-ttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
| ||| | | || | |||||| | | | | || | || ||| || |||| | | | || || | || | ||||||| || ||| |||| ||||||||||| ||||| |||||| |||| || || ||||||||||| |||||||||| || ||||| ||||||||||||||||
aacataatgaagggctatccttttaaactataggcaaagtgatgttgagaaatatct--gttgattagtgatcatc-tgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
-attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctc-tttgtggattgtttggtgtaacggattccctgaatgttctttg-cagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
|| | | | | |||| | || || | | || | | |||| || || | || ||| | || | || |||||||| ||| |||| |||||||| || ||||| || || | || || || || |||||||| |||||||||||||||||||| || || || |||||||
tgtttacttctgttaattttttaatgccttgttta--ttaatagttgtacaccaaatttgccatctgattt-catcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctc-tttgtggattgtttggtgtaacggattccctgaatgttctttg-cagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
|| | | | | ||| || || ||| | | || | | ||||| | | | | || ||| | || | || ||||| || ||| |||| ||||||||||| ||||| || || | || || || || |||||||| |||||||||||||||||||| || || || |||||||
gtttacttctgttaatttttgaatggcctt-gtttatttatagttctacaccaaatttgtcatctaactt-tatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------attgaaatataa-aggggtcataataaacta-agtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
|||| || | | | | || ||| || | | || | || | | ||| | | || | | | ||| || || |||||||| ||| | || || ||||| | ||| || ||| | ||||| |||||||||| |||||||||||||||||||| || || || ||||||||
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgct-ttttctttctcctcgtactgactaaggcta--gatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
gtgtaac putative branch site (score: 3)
tgttcttt putative PPT
attgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
- - -aatataaa
- - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - ggtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg