Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcctctcatttactttgtctgagtcagttttagagtttagagtgtaatggtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16440.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g53750.1 (Oryza sativa), 3'ss of exon 2
-gtttgtcctctcatttactttgtc---tgagtcag-----ttttagagtttagagtgtaatggtttatgtatac-gattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
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gttttctttactaccttgcactgttcattcaatcagcagcttgtccaaatccaaataatgctgactgtttcattttaatcccatagTGGTTGCATAACATCAGCAGAAACAGTTATGCTTGAGAAGCAAAGCTTGGGTGACTTCATTACTCGCATCAACTCTGACAAAGCTGTCATAGTATCGGTC
upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g53750.2 (Oryza sativa), 3'ss of exon 2
-gtttgtcctctcatttactttgtctg---agtcag-----ttttagagtttagagtgtaatggtttatgtatac-gattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT-----------------
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gttttctttactaccttgcactgttcattcaatcagcagcttgtccaaatccaaataatgctgactgtttcattttaatcccatagtggttgcataacatcagCAGAAACAGTTATGCTTGAGAAGCAAAGCTTGGGTGACTTCATTACTCGCATCAACTCTGACAAAGCTGTCATAGTATCGGTCTCTCCACAGTCAAGAGC
upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
---------------------------gtttgtcctctcatttactttgtctgagt-cagttttagagtttagagtgtaatggtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
|| | | | | || | |||| ||| || ||| ||| || | || ||||| | | | | || |||||||||| |||||||||| |||||||||||||| ||||||||||| || || |||||||| | ||| ||| |||| |||| ||||||| ||
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaactttta--tttggaatc--ataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
---------------------gtttgtcctctcatttactttgtctgagtcagttttagagtttagagtgtaatg---gtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
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tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0508g00020.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------gtttgtcctctcatttactttgtctgagtcagttttagagtttagagtgtaatgg---tttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
||||| | | |||| || || |||| ||| | | | || | || | | | | || |||||||||||| |||||||||||||| || ||||||||||||||||| | || |||||||||| | | ||| |||||| |||| || |||| ||| ||
tctaaaattttggttatgaaaagatttgt--taaaggtggcttttcttgggtaagttatagcaatatggacatcatagaatttaacctttttaacgatgcagTGGATGCATAACATCAGCTGAGACTGTGATGCTTGAGAAGCAAAGTATGGATGAGTTTCTCTTTAATATTAACAAAGGGAAGGCAGTCATTGTCTCCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctgagtcagttttagagtttagagtgtaatggtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
tttatgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcctctcatttactttgtctgagtcagttttagagtttagagtgtaatggtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG