Sequence
atgc intronic sequence ATGC exonic sequence...acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34660.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
acatactctttaaaagtcaattaatgtcatggtgttcacttggttc-tttctttattgcggtttggctactacaat-catatgtcaatcc---tgaatt--tgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
| | ||| | || |||| || | | |||| || | ||| ||| | | | | |||| | | | | || ||| | | ||||||| || || | |||| |||||| |||||||||| |||||||||||| | || ||||||||| | || ||||||||||| |||||||||||||| |
---ttacccgtaagtgcca--taatatcctttcat--acttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaat-ttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
| || | | || || || | | || || | | | ||| | | | ||| | | | | | ||||||| || ||| | | || |||||| |||||||||| ||||||||||| | || || || ||| | || ||||||||||| |||||||||||||| |
-atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 4
acatactctttaaaagtcaattaatgtcatggtgttcacttggt-tctttctttattgcggtttggctactacaatcatatgtcaatcctgaattt--gttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
| ||| || || | || | || | || || | || | | | || | | |||| | || | ||| ||||||||| ||||||||| |||||||||| ||||||||||||||||||||||||| |||||||||||||| |||||||||||||| || ||||| ||||| |
-cgctatctatactggt-ggctcatattattg-atttacctagtgtgtgttgccatcttagcctaataactatgtgattgaagtcatggtcaatgccgattagGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTAGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCGGAAGCCC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 4
acatactctttaaaagtcaattaatgtcatggtgttcacttggt-tctttctttattgcggtttggctactacaatcatatgtcaatcctgaat--ttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
| ||| || || | || | | | || || | || | | | || | | | || | || | ||| | ||||||||| ||||||||| |||||||||| ||||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||||||||| |
-ctctatctatactggt-ggctcatattgttg-atttacctagtgtgtgttgccatcttagcctaataattatgtgattgaagtcatggtcaatgctgattagGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
acatactctttaaaagtcaattaatgtcatg-gtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
| || || | | ||||||| || | ||| | || || | || | || || | | || | | ||| | ||||||||| ||||| ||| | |||||||| |||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||| ||||| |
atatgctggctcattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtg-aacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 4
acatactctttaaaagtcaattaatgtcatg-gtgttcacttggttctttctt-tattgcggtttggctactaca-atcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
|| || | | ||||||| || || ||| | || || | ||| || | || || | | | || || || | ||| | ||||||||| ||||| || | |||||||| |||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||| ||||| |
-tatgctggctcattgtcaatttatccaatttgtgcttgattttttttatctggcataatgtttctgcgagtgaacattttaagtattgcttga--tgcttagGTTGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCAC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 4
---acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
| | | || | ||| | | | | || | | | ||| | | || || | | || | || || |||| |||||| || || ||| | |||||||| |||||||||| |||||||||||| |||||||||||||||| ||||| |||||||| |||||||||||||
ttaagacatatttacattatcattctaaattctc-catttaatagtcagtttttcacctttataatgtgtagt-tatccagtgtttgattctttattt-ccagGTTGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTC
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
--acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
||| ||| | ||||||| || | | ||| | ||| | | | | | ||| |||| |||||||| ||||||||| | || ||||| ||||||||||||||||||||||| |||||||||||||||||||||| |||||||| ||||||||||||||||
cgtgccactttttcattttcaattattgctcctct-cctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgattt-ctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTCMapped 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|47831064|gb|CK120748.1|CK120748EST: CACAAATGGAGAAGGAACGTGGAAATATGTTGAAGGCTCTTGGTACACAG GTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCT
genomic: CACAAATGGAGAAGGAACGTGGAAATATGTTGAAGGCTCTTGGTACACAGgtttgtcttt ... aatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
aatttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC