Sequence
atgc intronic sequence ATGC exonic sequence...aggcttcttgggcatcaccttatgggatcctgattacactaacttctggttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60040.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 16
----aggcttcttgggcatcaccttatgggatcctgattacactaacttctggttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
| | || | || | || | ||| || | || || | | | | || | | | | || | | ||||| ||||| ||||| |||||||| ||||| | ||| | |||||||| ||||| ||||| || || |||||||| ||||||||||| ||||||||||||
ttcaacttgttctgactgcaattttgtttgaattaaaggtcacgaaatc---agcacattttggtatattcacatacaaatat-gttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G080176_T01 (Zea mays), 3'ss of exon 16
--aggcttcttgggcatcaccttatgggatcctgattacactaacttctgg--ttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
| | | || |||| || || | | | | || || | | | | ||||| | | |||| | | |||||| |||||||||||||||||||| ||||| | |||| | ||||| || || |||||||| ||||| |||||||||||||||||||| ||||| || |||
aatgaatctgccatttttactttataatttcaaaatgaagtagatatttaaatttgttaacacaaaaac----attctgataaggttttgtcttccatttgcagGCTAAAGGTTTTGTTGCTAATTCATTCTATACTGGTTTGACTGCTACTGAGTTTTTCTTCCACACAATGGGTGGACGAGAAGGTCTTGTTGACACGGCG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 14
----aggcttct-tgggcatcaccttatgggatcctgattacactaacttctggttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
|| || | || || | |||| ||| || | | | ||| || | | | ||||| | |||| | |||||| |||||||||||||||||||| || |||||||| | | || || || |||||||| || || ||||| || |||||||| || ||||||||||||
gctcagttttaaatatctattgttgaatactaccctggttatgtgaaacaactgacagttgtttcttagattgaatactgatatgctgtcctt-----gatgcagGCAAAAGGTTTTGTTGCTAATTCCTTTTACAGTGGATTGTCAGCTACTGAGTTTTTCTTCCATACAATGGGAGGGCGAGAAGGGCTTGTTGATACAGCG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv06s0004g03740.t01 (Vitis vinifera), 3'ss of exon 16
aggcttcttgggcatcaccttatgggatcctgattacactaacttctggttacta-ctttgagagct---aggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
| | ||| | | | || | | | |||| ||| | || || || ||| | | | | || |||| | | | |||||| |||||||||||||| | ||| ||||| | |||| | || || ||||| ||||||||||| || ||||| |||||||||||||| |||||||| |||
cagatctttg----ttatgtatccaaatgattaatgcactgactgcctattgatagctatgaactttcaaaagcatttaatggaatgttgtaatcttaatgcagGCTAAAGGTTTTGTTGCCAGTTCATTCTATACTGGTTTGACAGCTACAGAGTTTTTCTTTCATACAATGGGAGGACGAGAAGGTCTTGTTGATACGGCG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S26_192V6.1 (Physcomitrella patens), 3'ss of exon 16
------------------------------------aggcttcttgggcatcaccttatgggatcct-gattacactaac-ttctggttactactttgagagc-taggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
| | || | | || | | || |||| ||| || |||| | || ||| | | || | ||| |||| || ||| | ||||| || ||||||||||| || || || |||||||| || |||| || || || || ||||||||||||||||||||||| || || || ||||| ||
gtaaagagtggattttgtacgaggctttttgatttgatgttttagatgacttacttctcattttgctcgattgtactgacattctttatgcttatttaatggtgtaataatttgagatcataact---tgcgagtgcagGGCAAGGGTTTTGTTGCGAACTCCTTTTACAGTGGGCTCTCTGCTACTGAGTTCTTTTTTCACACTATGGGTGGACGAGAGGGACTTGTGGATACCGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
ccctgat putative branch site (score: 4)
tcttcttgcc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggcttcttgggcatcaccttatgggatcctgattacactaacttctggttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - catcacc
- - - - - - - - - - - - - - - - - -acactaa