Sequence
atgc intronic sequence ATGC exonic sequencegtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68060.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
-----gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaa-----ctgatgaaggaatatttcttgctcta-cttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| ||| | | | || | | ||| ||| ||| ||| | | || ||| | | | |||| ||| |||||| ||||||||| || |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||| |||||| |
gtaacatcctttactgttgctttcggataatcttcactgt-tctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 6
gtaagttaatacat--ttccgaaaaaagaagtatagaatctttactcaac-tgatgaaggaatatttcttgc-----tctacttttgc-------agGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
|||| ||| | || | | | || || |||| || || | || | || || ||| | |||| ||| |||||||| | ||||||||||| || ||||| || ||||| |||||| | ||||| |||||||| |||||| |||||||||||||||||||| |||||||
-----gtaatgcatgatgccctgagcacacgttcctgatgtttattctacctaatagaatggtaattgatgccaatttacacttatgctgatgtcagGAAGAAAGGAAAACTCTTGATCGTGAACTAGCTCGTGCGAAGGTTTCGGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 6
--------------gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttc--------ttgctctacttttg----------cagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| || | ||| | | | || |||| | | || | ||||| | ||| || | || ||| ||||| || ||| || ||||| | |||||||| |||||||| |||||||||||||| ||||| |||||||| || || ||||||||| |||||| |
gtaacaacctattctttgactattgcatatgtcatcatgtcttcatgagctcttccccc--cttctataggaacagttcactcatgcttatttaacatttatgatcattaccagGACCAAAAAAAGACACTTGAATGTGAACTTGCTCGTGCAAAAGTTACAGCAAACAGGGTTGCTGTTGTGGTTGCCAACGAGTGGAAAGATTCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 6
--------------gtaagttaatacatttccgaaaaaagaagtatagaatctt-tactcaactgatgaaggaatatttcttgctc-tacttttg-------cagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| ||| | ||||| | ||| || | | || ||| | ||||| | ||| |||| | ||| || |||||||| | ||| |||||||| |||||||| |||||||| |||||||||||||||||||| | || ||||| ||||| ||||||||| |||||| |
gtaacaaactatcatttgattacttcatttgccttcaaattcgtgtcattttttacacttttcacatgaacacttgattcatgcttatgcttatgattttattagGAAGAAAAGAGAACACTTGACCGTGAACTTGCACGTGCAAAAGTTACAGCAAACAGAGTTGCTTCTGTTGTTGCTAATGAGTGGAAAGATTCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G039325_T01 (Zea mays), 3'ss of exon 6
------------------gtaagttaatacatttccgaaaaaagaagtatagaatcttt-actcaactg---atgaaggaatatttcttgctct--------acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| |||| | | ||| | ||| | | | | ||| || | | ||||| | ||| |||| | ||| |||||||| | ||| |||||||| |||||||| |||||||| |||||||||||||| ||||| | || || || ||||| ||||||||| |||||| |
gtaacaaactatccttagattggttacttcttttgccttcaaatccatgtcaatttttttacccttttcaacatgaacacttgattcatgcttatgtttatgattttattagGAAGAAAAGAGAACACTTGACCGTGAACTTGCACGTGCAAAAGTTACAGCAAACAGGGTTGCTTCTGTTGTGGCCAATGAGTGGAAAGATTCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 2
-------gtaagttaatacatttccgaaaa------aagaagtatagaatctttactcaac-----tgatgaaggaatatttctt---gctctacttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| | | | | | ||| | | | ||| || | |||| | ||| || | | ||| | | || |||| ||| ||||||||||| || || || || |||||||||||| ||||||| || ||||| |||||| |||||||| ||||||||||| ||||||
gtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCAAATAGGGTTGCAGTAGTGGTGGCAAATGAGTGGAAAGATGGCGATGATA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
gtaagttaatacattt-ccgaaaaaagaagtatagaatctttactcaact---------------gatgaaggaatattt-----cttgctctacttt-------tgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
|||| | ||| || || | | | || | ||||||||| | | || | || ||| | || | | ||| | |||||||| ||||||||||||||||||| | || ||||| ||||| |||||||||||||| || |||||||||||||||||||||||||| |||||| |
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
----------------------------------gtaagttaataca-tttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
|| ||| | || || | | || || | | || || || || | || | || | | ||| | |||||||| |||||||||||||||| || | || ||||| ||||| |||||||||||||| || |||||||||||||||||||||||||| |||||| |
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcat--cttaattgttgcatgatttgttttgacacta----tatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
---------------------gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaat--atttct---tgctctact------tttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| | ||| | || | | || || |||| | | | || || |||| | || | || | | | |||||||| |||||||||| ||| |||| | || ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||| |||||||
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
---------------------gtaagttaa----tacattt-ccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctact------tttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
| | ||| | |||||| | | | | || || || | || | | | || | | | || | | | |||| ||| |||| ||||| ||| |||| | || ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||| ||||||||
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtaagttaa----tacatttccgaaaaaaga-agtatagaatctttactcaactgatgaaggaatatttcttgctctacttttg-----cagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
|| | || | || |||| | | || | ||| | | || | || | | | | | | | ||| | ||||| ||| ||||||| || ||| |||| || || ||||||||||| || |||||||| || || ||| || ||||||||||||||||||| |||||| |
gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaat--atttcttgctctacttttgc----agGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
||| | | || || | | | | | | | |||| | ||||||| | || ||||| |||||||| |||||||| ||||| |||||||||||||| || || |||||||| |||||||| |||| || || |
------------------------------gtagtgccgccagccacctttgggtcgcactcaccccacattgtctttttaccattagGAAGAGAAACGGACGCTTGAGCGGGAACTGGCGCGTGCCAAGGTAACAGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACAMapped 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|47831253|gb|CK120937.1|CK120937EST: CTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAAC GAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
genomic: CTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaat ... acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
EST:
gi|124737755|gb|EH829157.1|EH829157EST: CAAGAGATGAAC GAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
genomic: CAAGAGATGAACgtaagttaat ... acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
EST:
gi|163986081|gb|ES077849.1|ES077849EST: AGCGGAAGTTTCAAGAGATGAAC GAAGAACG-AAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
genomic: AGCGGAAGTTTCAAGAGATGAACgtaagttaat ... acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
aactgat putative branch site (score: 3)
tttcttgctctacttt putative PPT
aatatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG