Sequence
atgc intronic sequence ATGC exonic sequencegttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54450.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
-------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaa------gactctctactgtttatt--agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
|| || || ||| || | | || ||| | || | | |||| || | | ||| || || | || |||||||| || || || || ||||| ||||||||||| || ||||||||||| |||||||||||||| || || || |||||||| || ||| |||||
acgaattacttggattcaagttatattatttatgtgcga-atcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
----------------------------------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaac--ggcttttattaagactctctactgtttatt--agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
|||||||| | | ||| | | || | ||| | | | ||| ||| || || |||| | ||||||||||| ||||| ||||| ||||| |||||||||||||| |||||| |||||||||||||||||||||| || |||||||||||||||||| |||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
----------------------------------------------gttggtgtc----ttaagattaattagtaatatgaa-attggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
||||| || || | | || || |||| ||| |||| ||||| || || | | | ||||||||||| || || ||||| ||||| |||||||||||||| |||||| |||||||||||||||||||||| || |||||||||||||||||| |||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcattattcaaacgaactaaatatatttgtattatgatgccttaatcttttttacctttcctaaatattatctgc-agGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
------------------------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
| ||| || || | || ||| | | ||| | | ||||| | || | ||| | | ||||||||||| ||||| ||||| ||||| ||||||||||| || |||||| ||||||||||||| ||||||||||| |||||||||||||| ||| |||||
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaa--aatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgt-agGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 7
-------------------gttggtgtcttaagattaattagtaatat----gaaattggtgcttatta--acggcttttattaagactct--ctactgtttat---tagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
|| || | || | | || | |||| | | || | | | || | || ||| ||| | || | |||||||||||| ||||| ||||| ||||| ||||||||||| || |||||| ||||||||||||| |||||||| || |||||||||||||| ||| |||||
gtagatatactatattatcattaaattcacacaatgactctgtttttcagccaaaatatattcataacaaaatgcattgtgtttttacttcacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
------gttggtgtctt-aagattaatta-------gtaatatgaaattgg--tgcttattaacggctttta---ttaagactctctactgtttat-tagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
||| || || | |||||| | ||| || | || || | || ||| | || | | | | || | || |||||||| ||||||||||| ||||||||||| ||||||||||||||| ||||| ||||||| ||||| ||||| |||||||| ||||| | ||||||
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
-gttggtgtcttaagattaattagtaatatg--aaattggtgcttattaacggcttttatta---------agactc-tctac-tgtttatt------agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
|||| | | || | |||| | |||| || ||| | | | | || || ||| || || | | | ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||| ||||| ||||||| || || || || |||||||| | || | ||||||
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaac--ggcttttattaagactctctactgtttat-tagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
|| | | | || || | | | || | | | || || | ||| | | | | | || | | | ||||| || |||||||| ||||| || |||||||| |||||||||||||| | ||| |||||||||| || || || ||||| || ||||| | ||||||
gtcaactccgatcaacctttctttcacgttgtttgatcccctgacttgatttttttgtcgatatttttcattttctcaacagagtgcagctttttaccatcaattgagttttcaagattattttgaacgctgtgtgcagGTATTTTTCGTATGAGCATTTTTACGTCATATATTGCAAGTTCTGGGAACTAGATTCAGATCATGACTTTTTCATAGACAAGGATGATCTCCTTCGATAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
|| |||| || |||||| | | | | | || | | | ||| | | | || || || || || ||||||||||||||||| || ||||||||||| ||||||||||| | ||||| || || | || ||||| || | || | |||||
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtg-tgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
tattaac putative branch site (score: 1)
ctctctact putative PPT
ttttattaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA