Sequence
atgc intronic sequence ATGC exonic sequence...ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G35910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 2
-ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
| | || | | | | | ||| | || | ||| ||| || ||| ||| | || | | || | |||| ||||||| ||||||| ||||| ||||| || ||||| || ||||| ||||||||||| ||||| || ||||||||||||| | | || || || |||| |
ttcattcatgttatgggcatctgttatggaataaaacaacttctgaggcct-tgcagtgttaggaacttaagctttatttcggttcgtctgttgttttcagGTTGACTTGGAGCACAATCAATATAGGTCATTTCAGGGTTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAGGATTTTGTTGTAGACACCCTTAAAC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 2
---ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
||| || || | || || | |||| |||| | | || || || || | | | | | ||| ||| | |||| |||| ||||||||||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| || |||||||| || | ||| || || || ||||||
atgttctaggctatctgacatgc-aatagaataaattcca--tggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 3
---ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
||| || || | || || | |||| |||| | | || || || || | | | | | ||| ||| | |||| |||| ||||||||||||||||| ||||| || ||||| || || || ||||||||||| ||||| || |||||||| || | ||| || || || ||||||
atgttctaggctatctgacatgc-aatagaataaattcca--tggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G452875_T01 (Zea mays), 3'ss of exon 2
---ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
||| ||| || | || || | |||| |||| | | || || || || | | | | | ||| ||| | |||| |||| ||||||||||||||||| ||||| || ||||| || |||| ||||||||||| ||||| || |||||||| || | ||| || || || ||||||
atgttctaggctatttgacatgc-aatagaataaattcca--tggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGATCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 2
---ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
||| || || | || || | |||| |||| | | || || || || | | | | | ||| ||| | |||| |||| ||||| ||||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| || |||||||| || | ||| || || || ||||||
atgttctaggctatctgacatgc-aatagaataaattcca--tggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTAGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G118917_T02 (Zea mays), 3'ss of exon 2
ctctccttgattagataagccaaaaaaatatattcaagtttgagt-tgccaatgc--ttatttctcccctttctcttaagttttttg--tttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
|| | || | || | | | | | || | | | |||| | | || || | || | ||||| || || ||| |||| ||| |||| || || || ||||| || ||||| || ||||||||||||||||| ||||| || ||||||||||| | ||| ||||| || ||||||
----atatgcatctatgcactgaacac-tgtttcttaattaaattattttgatgcactgagcactgtttattaattaaactattttgacccttccatcatttcagGTCGATTTGGAACACAACCATTATAGGTCGTTTCAGGGTTTGACATGCTTGATGCAGATTTCAACAAGAACAGAGGACTTTATTGTTGACACTCTTAAGC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 3
-------ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
|| |||| || | | || ||| | | |||| | ||| | ||| | | | | ||| ||| | | ||||||||| |||| |||||||| ||| | ||||| ||||| ||||| ||| ||||||||||||| || || || || |||| ||| ||||| ||||| || |
gctgatattcccctttcttgtagtcactccctccattacttccattc---attgc----attcttttgacttatttatgtataatgacttgaagttgaaatgtatagGTTGATTTGGAACATAATCAATATCGGTCTTTCCAAGGTTTGACTTGCCTGATGCAAATTTCAACAAGGACTGAAGATTTTATTGTTGACACATTGAAAC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G29260.1 (Glycine max), 3'ss of exon 2
ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccct-ttctcttaagttttttgtttttgctc----tttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
|| |||| | ||| | | | || || | | | ||| || | |||| || | ||||| | || | | || |||| ||| |||| |||||||| ||| | ||||| ||||| ||||| |||||||||||||| || ||||| || || |||| | | | ||||| | |||
----atttaattat-tgtcccagtattctctcttttagatacttctcctgtccctttctttcattatattcttttgacatttttatcttgacgtggaatgttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
-------ctctccttgattagataagc-caaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
| | | || | || || || || || ||| | | |||| | | | | ||| || |||| | ||||||||||| ||||||||||||| ||| | |||| ||||| ||||| ||| |||||||||| || || || || || |||| ||| ||||| || || || |
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgacctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 1
ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctccc--ctttctcttaagttttttgttttt---gctctt-tttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
| | | | | | | ||| || | ||| | | | | | | || | | || | | | || | || |||| || || | |||||||||||||| |||||||||||| ||||||||||||| ||||| |||||||||||||| || || || || ||||||| | | ||||||||| | ||||
----ctatcactt--ctaacaagaaatttacgtgcaaataatatgtacataatgtcatctggactagctaattttcaggtctctttctttttgaactattgtctagGTTGATCTGGAACATAATCAGTATCGATCTTTTCAAGGGTTGACTTGCTTGATGCAAATCTCTACTAGGACTGAGGATTTTGTTGTTGATACACTAAAGCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116454660|gb|EG497252.1|EG497252EST: AAGATCTGAAAGAATTAGTTGCCAAACTGCGTAGTGTTGAAGAGTTTGCG GTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTG
genomic: AAGATCTGAAAGAATTAGTTGCCAAACTGCGTAGTGTTGAAGAGTTTGCGgtaaatttct ... ctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
tttctcccctttctct CT-rich tract
ttaagttttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
ctctcct
- - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - agtttga