Sequence
atgc intronic sequence ATGC exonic sequencegtgaagtccttactattatccaatctgtttctcattgagactttgtctatgtatgaaccgcctcctacttcccatggaaacatctgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17940.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G29110.1 (Glycine max), 3'ss of exon 9
gtgaagtccttactattatccaatctgtttctcattgagactttgtctatgtatgaaccgcctcctacttcccatggaaacatctgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
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-------------------------tctttattctatatggtctatttatgtggtgtgcattagtaatttaacatgggtgcttttga--tcagcatacattgagttgattacattgttttttt--------acagGCTCAAGATAACATTATGAATCTTCCATTAGCAAATGGTTGGGGTGAAAAACATTGTCTTTTTGTGAAATGGAAATATGTTGAAGCAAAG
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G33650.1 (Glycine max), 3'ss of exon 7
gtgaagtccttactattatccaatctgtttctcattgagactttgtctatgtatgaaccgcctcctacttcccatggaaacatctgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
| | | | | || || |||| | || || | | || ||||| ||| ||| | | || | | | |||| | | |||||| |||||||| | |||||||| ||||| |||||||||||||| ||||| ||| | || ||||| || ||||| ||||||||||| |||
------------------ctctgcttatgtgtgtgtgtgaacttgtatgtgcattagta-------atttaacatgggtgcatttga--tcagcatacattgagttgactacattgtttattt--------acagGCTCAAGATAACATTATGAATCTTCCGTTGGCAAATGGTTGGGGTGAAAAACATTGTCTTTTTGTGAAATGGAAATATGTTGAAGCAAAG
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 9
gtgaagtccttactattatccaatctgtttctcattgagactttgtctatgtatgaaccgcctcctacttcccatggaaacatctgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
|| | | | | | | | | | |||| || | | | || |||| | ||| | || | | | ||| ||| | ||| | | ||||| ||||||||| | ||||| || || ||||||||||| ||||| ||||||||| | || ||||| || ||||||||| ||||||| |||
------------------------ctatataccgt-gtaagtgtatgcatgtgtgtgcattagcatg-ttaacatgaatgcattt--aactgacaaacattactttatttacactgttcatttt-------gcagGCTCAAGATAATATTATGAACCTTCCATTAGCAAATGGATGGGGTGAAAAGCATTGTCTTTTTGTGAAATGGAAGTATATTGAAGCGAAG
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G31710.1 (Glycine max), 3'ss of exon 9
gtgaagtccttactattatccaatctgtttctcattgagactttgtctatgtatgaaccgcctcctacttcccatggaaacatc--tgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
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---------------------------------ctatatactgtgtatgtgtatgcat-gtgtgtgcattagtatgttaatatgaatgcatttaaccgacaaacattactttatttacactgttcattttg---cagGCTCAAGATAATATTATGAACCTTCCATTAGCAAATGGATGGGGTGAAAAACATCGTCTTTTTGTGAAATGGAAGTATATTGAAGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
tgttaat putative branch site (score: 3)
aaattttttgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagtccttactattatccaatctgtttctcattgagactttgtctatgtatgaaccgcctcctacttcccatggaaacatctgaaattttttgttaatgcttccttttccttgtcggtgtgcgctgaaacagGCACAAGATAATTTAATGAATCTCCCGTTAGCAAATGGTTGGGGAGAAAAGCATGGACTCTTTGTTAAGTGGAAGTATGTTGAAGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC