Sequence
atgc intronic sequence ATGC exonic sequencegtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctcttgttttatatttatctgttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61980.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtca-----catctttatactctcttgt-----tttatatttatctgttgatataactgtt--cttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
||| | | || |||| || ||| | || || |||| || | | | | | || || | || | || | | | | | ||||||| ||||| || ||||||| ||||| || || || || ||||||||||||||||||||||||||||| |||||| | ||||||||||| || ||| |||
gta-gcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtc-atattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctc-ttgttttatatttatctgttgatataactgt-tcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
| ||| || || | | | | | ||| || | | || | || | || | | || | | | ||||||| ||||| || | ||||| || || || ||| | || ||||||||||||| ||| ||||||||||| || ||| |||||||||| || || ||||| |
--------------------gtaccacttcctggttcactaggaattaaagcttcatgcagacattctagtactgtcattcctgaaacaaagtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 11
gtaaggaaatatcttttg----tattgaggcttactcgtcaaactgctgtcacatctttatactctcttgttttatatttatctgttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
|||| | || | |||| | || | | | || | | ||| | | | | ||||||||| | | || | |||| || ||||||||||||| || | ||||| ||||| ||||| | || ||||||||||||||||| |||||||| || |||||| |||| || || || || ||| | |
tgctggaactctccaaagacaatattcatgcatgcatgattaagtaatttcataaaagaagatgca--tgttttatactgaaacgt--aaggaactatt-ttcagGTTCAGACCATTCGCCAAGGCTATCTATCTAAGAGATCTTCAAACTTGAGAGGTGATTGGAAAAGGAGGTTCTTTGTCCTCGACAGTCGAGGAATGTTGT
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
---------gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctc--ttgttttatatttat--ctgttgatataactgtt------cttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
|| | || || | |||| ||| | | | | | | ||| | ||| ||| | | | || | ||| | | | || || ||||||| | || ||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| | ||| | |||| || || || ||| | |
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
----gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctcttgttttatatttatctgttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
|||||| ||| | || || | ||| | | ||| | || | | || || | | | || | |||| | || | || ||||||| | || ||||||| ||||| || ||||| |||||||| ||||| ||||||||||| ||||| | ||| | |||||||| || || ||||| |
gtatttaaggacataa-tgatgc-ttcacactttcacttca---ttctatatagttttcatttatgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------gtaaggaaatatcttttgtattgaggcttactcgt--caaactgctgtca--catctttatactctcttgttttatatttatct-gttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
| | | | | || | || || | | | | | ||| | | |||| | | || |||| || ||| | | | | | | | | | |||||||| || || ||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||| |||||| | ||||||||||| || ||| | |
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S249_58V6.1 (Physcomitrella patens), 3'ss of exon 6
------------gtaaggaaatatcttttgtattgaggcttact-------cgtcaaactgctgtcacatctttatactctcttgttt-tatatttatctgttgatataactgttcttca--gGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
| | ||| | | | | |||||| | | || ||| | || | | ||| ||| |||| | | | || | | | || | | | | || || |||| ||||| || | | || ||||||||||| ||||||||||||||||| |||| || ||| | || ||||| | || ||| | |
gtaggaatttgagctgaggaattctaaatatgtagttgcttacgatacgggcttaaagctgaaaacgcagacctttttatccttatttacatatctgtttatttttttcttttttacttatagATACAAACCATCAAGCAAGGATACATTTTGAAGCGTTCCTCAAATTTGAGAGGTGACTGGAAGCGAAGGTTTTTTGTGCTGGATAGTAGGGGAATGTTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacatctttatactctcttgttttatatttatctgttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
atataac putative branch site (score: 3)
ctgttcttc CT-rich tract
ttgttttatatttatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctcttgttttatatttatctgttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG