Sequence
atgc intronic sequence ATGC exonic sequencegtaagttacgctatcagttagagttagaatagtttcatctttccattgtttagaatttaattgacacaactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65430.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 6
gtaagttacgctatcagttagagttagaatagtttcatctttccattgtttagaatttaattgacacaactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG
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----------------gtgagtgctgaaactgattagtt----catt-tttaca--taatctgcagtgagcagaccatat-attttcttctt------ttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G431691_T01 (Zea mays), 3'ss of exon 5
gtaagttacgctatcagttagagttagaatagtttcatctttccattgtttagaatttaattgaca-caactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG-----------
|| || ||| || | || | |||| || | |||| || | | ||||| | | ||| || | | | ||||| | || |||||||| ||||| |||||||||| ||||||||| |||||| | | ||||| ||||| ||||| ||||||||||| ||
----------------gtgagtgttgaaactgattagtt----cattttt----acataatcagcagtgagcaaaccatat-attttcttctt------ttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGATTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCAGAGAATATGAACTGGTATAGAAGGA
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 6
gtaagttacgctatcagttagagttagaatagtttcatctttccattgtttagaatttaattgacacaactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG
|| || | | || | || | |||| || | |||| || || ||| || | | | || | ||| ||| | || |||||||| ||||| ||||| |||| ||||||||| |||||| | | ||||| ||||| ||||| ||||||||||||||
----------------gtgagtgctcaaactgattagtt----cattttt----acataatcagca-gaccatat-attttattctttttttca----------gTGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCAGAGTCAGAGAATATGAATTG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G143644_T01 (Zea mays), 3'ss of exon 6
gtaagttacgctatcagttagagttagaatagtttcatctttccattg--tttagaatttaattgacacaactataccatgtcactttta-----tcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG-----------
|| || ||| ||| ||| | || |||| ||| || || | || | | || || || || ||||||| |||| |||||||| || || || | || || ||||||||||||||| |||| ||||||||||| || || || |||||||| ||
-----------------------gtacgatggttccattcttctaatgattttatgcttttgttcacgagtcctagggattgagcatctaaggcctcatctcttgtttgcagTGCACTGAGGAAGCTCATCGACCAGTGAACTGCGAGACTGTTTCTAAGTGGATATTAAAGAATAGTGCAGAATCTGAAAATATGAACTGGTTTGTCGCAG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G157933_T01 (Zea mays), 3'ss of exon 5
gtaagttacgctatcagttagagttagaatagtttcatctttccattgtttagaatttaattgaca-caactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG-----------
|| || | | || | || | |||| || | |||| || | | ||||| | | ||| || | | | ||||| | || |||||||| ||||| ||||| |||| ||||||||| |||||| | | ||||| |||| ||||| ||||||||||| ||
----------------gtgagtgctgaaactgattagtt----cattttt----acataatcagcagtgagcagaccatat-attttcttctt------ttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGTGGAGTCAGAGAATATGAACTGGTATAGAAGGA
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttacgctat-cagtta--gagttagaatagtttcatctttccattgtttagaatttaattgacacaactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG
|| ||| | || ||| || || | || ||| | || | | || || | | | || || | | | || |||||||| | || ||||||||||||||||| ||||| | |||||| | |||||| | |||||||||||||||||||| ||||| ||||||||
gtgagtatccttaaattgttgatgaatttgtctattttgaaaagcttcttttgcccatcttgttttgtgtatgtgtgtgataca--ttatgtgaacttgaacttgcagTGTACAGAGGAAGCTCACCGTCCTGTTGATTGCGGCACTGTGGCCAAGTGGATTTTGAAGAATAGTGCTGAGTCTGAGAACATGAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaatttaattgacacaactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG
aattgac putative branch site (score: 3)
tttaattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttacgctatcagttagagttagaatagtttcatctttccattgtttagaatttaattgacacaactataccatgtcacttttatcgtcatgggtctgcagTGTGCTGAAGAAGCTCACCGTCCTGTAGATTGTGACACTGTTTCTAAGTGGGTATTGAAGAATAGTGCTGAGTCGGAGAATATGAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA