Sequence
atgc intronic sequence ATGC exonic sequence...aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g38834.1 (Oryza sativa), 3'ss of exon 2
aatttatgaattatgatttaaacgataccacctacacatgtaagcaactata-ctgtgtagctcg------aaagagtaatatgtaacctaaatg---tgatacgtgtagAGAGA----TGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| || ||| | || | | | | || | | ||| | | | |||| | | ||| || | | | ||| || | || ||| || |||||||||||||||||||| | |||||||| ||||||||| | | |||| |||||| ||||| ||||| ||||| ||| | || || |
gtttaattaatcttcatacatatatacttaatttcatgcatgcatagctagatcaatcgagctagctatatatagatcgatgctgatcatgcatggattggggtgggtgagaagAGCATTGCAGGATAGGGTACGAGGAGCAGAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGAT
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G025642_T02 (Zea mays), 3'ss of exon 2
-----------------------aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| ||| | | | | || || || || | || | | | | | | | || ||| | | || | || |||| |||||||||||||||| |||||||| ||||||||| | | ||| ||||| || || ||||| |||| ||||| |||||| |
gtacgctagctagccgcagctccggccagcctgttccgatccggcctgt-cgatctgaac-tgctggcgatgatcttaaatttcctgctctggctggctctgctctcaatctctca-----agGGCATTGCGGGATCGGGTACGAGGAGCAAAACGAGTGGTACTTCTTCAGCTACAAGGACCGCAAGTACCCCACGGGGACGCGGACCAACCGGGCCACCAT
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
-aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| | ||| |||| | || | | | | | | | ||| | || | ||| || | || ||| || ||||| || ||||| |||||||||||||| | |||||||||||||| ||||| | ||||||||| ||||| |||||||| || || ||| |||||||| |
ttgttaaagaaatatggtc-aagctagatcttaattagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
-------aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| | ||| |||| | || | | | | | | || | || | | || | || | | | | | || | ||||| ||| ||||| |||||||||||||| | |||||||||||||| ||||| | ||| ||||| ||||| |||||||| || || ||| |||||||| |
atcatattgttaaagaaatatggtctag-caaagctagatcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttg------gcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgt-agctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| | ||| || ||| || || | |||| ||||| ||| || || | | | | | | ||||| | | ||||||||| ||||||||||| || ||||| | |||||||||||||||||||| | ||| || |||||||| || ||||| || || || |||| ||| |
catatttgatctaacattataattattatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctgatgtgaatgatatg-gcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatg--tgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| | ||| | || | || | | || | |||| | | ||| | | | | | | | | || ||||| | | ||||||||| ||||||||||| || ||||| | |||||||||||||||||||| | ||| || |||||||| || ||||| || || || |||||||| |
-atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaatgatatg-gcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-------------------aatttatgaattatgatttaaacgat-accacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
| || | | || || ||| | | | | | || | ||| | | | || | | | | || || ||| | || | || || | || |||||| |||||||| ||||||||||| | ||||||||| || ||||| ||||| ||||| ||| |||||||||
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
------------------aatttatgaattatgatttaaacgataccacc---tacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
|| | ||| | ||| | ||| | | | | || | ||| | | | || | | | | || || ||| | || | || || | || |||||| |||||||| ||||||||||| | ||||||||| || ||||| ||||| ||||| ||| |||||||||
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
acctaaa putative branch site (score: 3)
taatatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - aacgata
- - - - - - - - - - - - - - cacctac
- - - - - - - - - - - - - - - - - - - - -aagcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacctaa