Sequence
atgc intronic sequence ATGC exonic sequence...ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G45620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 1
---ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
|| | || |||| | | || | ||| | | ||||| || ||| | || ||| | | | || || || | ||| | ||||| | | || ||| |||| |||||||||||||||| || |||||||||||||||||||| || ||||||||||| || || | | || |
aaatttactcttgttgtttgaaccttgcttaggtttgtaactgctgtgttgtgcct--tctgcgtttttgcaattctaacagcggcatccattctc-ctacagACGGGTGACACCCTCATACAGCTCTACAACAATTTCATCACTGATTTCGAGACGAAGATCAATCTTCTCAAACTTGCGCATTTCGCGGTCATCGCTTCGC
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
ttaggttttagggtttatagatcaattttg-attgcttc--caagtttttgtgtctgatcttaacctgtgt-cattgttataatataattttttttcattt-----cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
| | || ||||| ||| ||| |||| ||| | || | | | ||||| || || | | ||| | |||||| ||| |||| || | | || ||| |||| ||||||||||| ||||||| |||||||||||||||||||| || ||||| || || || || | | || |
---------tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 2
ttaggttttagggtttatagatcaattttgattgcttc-caagtttttgtgtctg-atcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
|| ||| || || || | | ||| | | | | | |||| | | | | | || || |||||| | |||| | | ||| | || || || | |||||| |||| |||||||||||||||| |||||||| ||||| ||||| || |||||||| |||||||| ||| | | ||||
-taaagtttgccaattttatattgttccaagtcatttcacctgctgctatttctgtactcttttgtcttttatgattctaatatcaccttttctt-ctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATCACTGATTTTGAGACCAAGATTAATCTGCTCAAGCTTGCCCATTTTGCGGTGATAGCTTCTC
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 1
-ttaggtttta--gggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcattt-cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
|| || || | ||| | | |||| | || || || | | | | | || | | | ||| | | | || | | |||| ||||||||||||||||| || || || ||||||||||||||||| |||||||||||||| ||||| ||||| |||||||| ||||||||||| | || ||||
gttgacttctattgaaacaatattcatactctgatg---tgcatattcttat-tatagtttaaatttatttgtttgacaaacggttcttcctataaattttcagGCTGGTGATGCTTTAATACAATTATATCACAATTTCATCACAGACTTTGAGACGAAAATCAACCTTCTCAAGCTTGCACATTTTGCTGTTATAGTTTCTC
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
-ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTT-CTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
| | | |||| || | | || ||| | || || |||| | | | | ||||| | ||| || | | | || | |||| || | | ||| || || || ||| || | | | | || | || || | | || | | |
gtgatgctttaa----tacaattatatcacaatttcatcacagactttgagacgaaaatcaacct-tctcaagcttgcacattttgctgttatagTTTC---TCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTT-ATCTTGGAG---GGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
ttaggtttta--gggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttca---tttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
| ||||| | ||| | | | |||| | || || || | | | |||| ||| || | | | || | || | | |||||||| |||||||| || || || || ||||||||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| ||||| | || ||||
-tgacttttattgaaacaatatttgtactctgata---tgcatgtgttcttattatagtttaaa-tgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcattt-cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
| | || | | | ||| | ||| | || || | | | || | | || || | | | | ||||||||| ||||| ||||||||| | |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||| || ||||||||||| | || |||
-ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTAMapped 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|152034147|gb|BP868636.2|BP868636EST: ATCAACTCACCCTTAAGCTCGAAAAGTTCATCGCTCTCGCTGTCTTTCAG GCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
genomic: ATCAACTCACCCTTAAGCTCGAACAGTTCATCGCTCTCGCTGTCTTTCAGgtacttttgc ... ttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
EST:
gi|116482621|gb|EG525213.1|EG525213EST: ATCAACTCACCCTTAAGCTCGAACAGTTCATCGCTCTCGCTGTCTTTCAG GCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
genomic: ATCAACTCACCCTTAAGCTCGAACAGTTCATCGCTCTCGCTGTCTTTCAGgtacttttgc ... ttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
tcttaac putative branch site (score: 2)
ttttttttcatttc putative PPT
tgtgtcattgttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- -ggtttta
- - - - - -ggtttat
- - - - - - - - - - - - - - - - - cttccaa
- - - - - - - - - - - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cttaacc