Sequence
atgc intronic sequence ATGC exonic sequencegtaggcatattttcttgattgccattttttttctccatatgtcatggtgatcttccacatttatattgagttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G06290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 2
----gtaggcatattttctt--gattgccattttttttctccatatgtcatggtgatcttccacatttatattgagttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
|| ||||||| | ||| | || | | | | || |||| | |||| | || | ||||| | ||||| |||| || |||||||| |||||| | |||||||| ||||| |||||||||||||||||||||||||||||| || |||||||| ||||||||||| |
gtatgtgatgatattttggtcaaattactgaattgtagttttgttagctgtgttgatg----agatttttcttt-gccttatttgactaatttga---agGTCCGAGGAATTGAGACAGTGGCTACTTATGATATTAAAACAAGAGAGTTTGTGATAAATACTCCTTGTGAATCAGCCCAGAAGTACTGGATTGGTGGAG
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 2
--gtaggcatattttcttgattgccat-tttttttctccatatgtcatggtgatcttccacatttatattgagttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
||||| || | | ||| ||||| | ||| || | | | | ||| | | | || ||| ||| || | | ||| || ||||| |||||| | |||||||||| || |||| |||||| | ||||||||||| |||||||| ||||||||||| ||||||||||| |
gtacgtgcatagatttgggctaagcatactttttacggtata-atctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaa--gGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
----gtaggcatattttcttgatt---gccattttttttctccatatgtcatggtgatcttccacatttatattga---gttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
|| | | | | | |||| | | || | || || | || | | | || | | || | | || |||||| || |||||||||||||| || |||||||| |||| || | || ||||| || |||||||| |||||||| | ||||||||||||||||||||| |
gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
----gtaggcatattttcttgatt----gccattttttttctccatatgtcatggtgatcttccacatttatattgagt---tctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
|| | | | | | | |||| || || | || || | || | | | || | | | | | || |||||| || |||||||||||||| || |||||||| |||| || | ||| ||||| || ||||| || |||||||| | ||||||||||||||||||||| |
gtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
gtaggcatatttt-cttgattgcc--attttttttctccatatgt-catggtgatcttccacattta------tattgagttctatttatttcttt--tgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
||| | | || ||||| |||| | ||| | ||| |||| ||| |||| | || |||| | || |||||| || |||| || || ||||||||||| || || |||||| ||||||||| ||||||||| || || | ||| |||||||| ||||||||||| ||||| || || |
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S37_122V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------gtaggcatattttcttgattgccattttttttctccatatgtc-atggtgatctt--ccacatttatattgagttctattt------att----tcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
| | | |||| ||||| | ||| || || | | || | || || | || | | | | | | | ||| || | ||| |||| || || |||||||| || || || ||||| || || || |||||| | || | |||||||| ||||||||||||||||| |||||||| || |
gtaagtactaggtcttttacggtttctctgtcctctcaaaactggtagtgagaatctgcaaagctatctgtctgtctagcgtttaacgtttttttgggattgataatttcccgatctatttttggattataattttattcgcagtgttgtgaaaattagtctttgaacattgtgatcctctgac-cagGTGCGAGGCATTGAAACTGTTACTACCTATGATCCTTCTACAGAGGAGTTTATCATCGACACTCCTTGCGAATCTGCTCAGAAGTACTGGATTGGAGGAG
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S149_61V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------gtaggcatattttcttgattgccattttttttctccat-atgtcatggtgatcttccacatttatattg-----agt--tct----atttatt--tcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
|| || || | | | ||| | | | || | | || || ||| | || || | ||| ||| || || | | || |||| |||| || || |||||||||||||| |||||||| | || || ||||| | || |||||||||||||||||||||| ||||| |||||||| || |
gtaagtgttggaatttcctaaggtcttttttgttgtctcaaaactgattggtatgaagctgaaactaattctaattgataggtgtcaattaatctttagaaccgatagtttactacacgattgtttgattgtaggctttccttttagcatcgtgaaaagtggtctcagaatatagtgattttctgat-cagGTGCGAGGCATTGAAACAGTGACTACTTATGATACTTCCACAGAGGAGTTCATCATCGATACTCCTTGTGAATCTGCTCAAAAGTACTGGATTGGAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatggtgatcttccacatttatattgagttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
ttttgat putative branch site (score: 4)
ttctatttatttcttt CT-rich tract
atttatattgagttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcatattttcttgattgccattttttttctccatatgtcatggtgatcttccacatttatattgagttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG