Sequence
atgc intronic sequence ATGC exonic sequence...tttcagataatacaagtaacttagttcttgaaactgtagtagttgccaggttcacattgtctttatttttctgacttctgtttgcatgttgtgcctccagAATCAGTTTTTCATATCAGGCCTTTCTGGAGATGACACAGTAAAGAACCGTGTCTTAGAAGCATTGTACAAGAGGATTTTGCGTGCCCATAACGAGAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16785.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 11
------------------------------------------------tttcagataatacaagtaactt-agttcttgaaactgtag---tagttgcca-ggttcacattgtctttattt--ttctgacttctgtttgcatgtt----gtgcctccagAATCAGTTTTTCATATCAGGCCTTTCTGGAGATGACACAGTAAAGAACCGTGTCTTAGAAGCATTGTACAAGAGGATTTTGCGTGCCCATAACGAGAAGA
| ||| ||| || | | | |||||| | | ||| || | | || ||| || | || | ||| | ||| || || | ||||||||||||||||||||||| ||||| |||||||||||| |||| |||||||| ||||||||||| |||| | | || | | || | || ||||| |
gtgctgaaccttttttaatctcttgattttcaaatgtaatccacaaactccaagaaaatttgtatatttggaagtattgaaatttcatacctagatgatacaatacagattcatttcacttggtctaaactctaagcttcattttactggtctatgcagAATCAGTTTTTCATATCAGGTCTTTCAGGAGATGACACAATAAAAAACCGTGTATTAGAAGCATTATACAGGCGTATACTTAGAGCAGAAAAGGAGAAAA
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 12
----tttcagataatacaagtaacttagttcttgaaactgtagtagttgccaggttcacattgtctttatttttctgacttctgtttgcatgttgtgcctccagAATCAGTTTTTCATATCAGGCCTTTCTGGAGATGACACAGTAAAGAACCGTGTCTTAGAAGCATTGTACAAGAGGATTTTGCGTGCCCATAACGAGAAGA
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aaaaaatcttttttttttgcacacatactccataagtatgtaattaatatcca--tgagactgcca--aattgttaacatcctatttgcgcaccttttttgcagAATCAATTTTTCATATCAGGCCTTTCAGGAGATGAAACGATAAAAAATCGTGTATTGGAAGCATTATACAGGCGCATACTTCGGGCAGAGAGAGAAAAAA
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G158008_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------tttcagataat--acaagtaacttagttcttgaaactgtagtagttgccaggttcacattgtct--ttatttttctgacttctgtttgcatgttgtgcctc--cagAATCAGTTTTTCATATCAGGCCTTTCTGGAGATGACACAGTAAAGAACCGTGTCTTAGAAGCATTGTACAAGAGGATTTTGCGTGCCCATAACGAGAAGA
|||| || | | || ||| | || | | || | | || || | || | || | || | || | | |||| ||||||||||||||||| ||||| ||||| || ||||||||| | ||||| ||||| ||||||||| | || | | | || | | || | || ||||| |
gtgtgttttcttagctctgcagttttaagccataagatttaagttttattgtaacacttgatattcagagttattcacgttcatatgtttgagaattaatagacctcatatttcgatatgcacatataattacaaatagactgatatcccttgtaacatacattcgttcttctggcctttgcagAATCAGTTTTTCATTTCAGGTCTTTCAGGGGATGACACAATTAAGAATCGTGTATTAGAAGCACTATATAGGCGCATACTTAGAGCAGAAAAAGAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaggttcacattgtctttatttttctgacttctgtttgcatgttgtgcctccagAATCAGTTTTTCATATCAGGCCTTTCTGGAGATGACACAGTAAAGAACCGTGTCTTAGAAGCATTGTACAAGAGGATTTTGCGTGCCCATAACGAGAAGA
ttctgac putative branch site (score: 2)
tgcctcc putative PPT
attgtctttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcagataatacaagtaacttagttcttgaaactgtagtagttgccaggttcacattgtctttatttttctgacttctgtttgcatgttgtgcctccagAATCAGTTTTTCATATCAGGCCTTTCTGGAGATGACACAGTAAAGAACCGTGTCTTAGAAGCATTGTACAAGAGGATTTTGCGTGCCCATAACGAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - aatacaa
- - - - - - - - - - - - - -ttgaaac