Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53430.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 19
gtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
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----gtaattctaatctttctaaggtggattatttgcttcagtggtcaatt-ttctgac--tgttttatgggtactttgtatgattccagAGAACCGAAAATGAACGGGTTTGCTTTGGTAGATCAGGCATACATGAATGGGGCCTCTTTGCACGAAGAAATATTCAAGAAGGAGACATG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 19
gtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
| | | || | ||| | | || | | | || || || || | | | | | || ||| | | ||||| || |||| || ||||| ||||||||| |||| || ||||| ||||||||||| ||||| | |||||||||||||||||||| |||
----gtaattcttctctttctaaggtggattatttgcttcagcagtcaatt-ttctgac--tgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 10
gtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
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----gtaaatctcctctttcttaagcagtcattgg-atttggtgatcggtt-ttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 19
gtaagcattcctcgcatatctgaaggag--actgtactatatagttgt-atcttg----ttgtaataacatctgacaagt-ttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
|||| ||| || | | | || | | | |||| | || | ||| || | | | | | | ||||| |||||||| |||| || |||| ||||||||| ||||||| |||||||| |||||||| ||||| || | ||||||||||||||| |||
gtaaattttcatcatttctgttcagcaattatcctcctatcaacttcttggattgacgatttttttttttttttgtatgcattcatacacgactccagAGGACTGAAAATGATAGGGTTTGCTTTGGTAGATCTGGAATACATGGCTGGGGCCTCTTTGCACGACAAGCTATTCAAGAAGGAGATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
ttgtaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA