Sequence
atgc intronic sequence ATGC exonic sequenceGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73350.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag
||||| ||||||||||||||||| ||||| || |||||||| ||||| |||| || |||||| | ||||| | | || | | || | || | | | || | | || || || ||
----------------------------------------ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAGgtatt--tcatgctctctgtttttttgtatgaatctgtgtaggttcctcattaact--ttgttttatgtgtcgatgttttttcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G146786_T02 (Zea mays), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag
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GGATTTTGGTTCTCT---ACTCGGTGGTTGATACCAACAGATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtat-----ttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcag----------
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag
|||||||||||||||||||| | |||||||| ||||| |||||||| |||| | | ||| || | | | ||||||| | | | | | ||||| ||
----------------------------------------ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtat-----ttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcag----------
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G33570.2 (Glycine max), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttt-------tttgtttttcgttcttctt-ttgtagttgtgtcatggccataattcttgagtttcttgtag-------------
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GGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCGgtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttt-taaaagtttaaatatgcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G33570.1 (Glycine max), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttt-------tgtttttcgttcttctt-ttgtagttgtgtcatggccataattcttgagtttcttgtag-------------
||||||||||||||||| || |||||||| || |||||||||||||||||||| ||| | || | ||||| | |||| | | |||| | || || | || ||||| ||| | ||
----------------------------------------ATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCGgtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttt-taaaagtttaaatatgcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag------------------------
||||| ||| | | ||| ||| | |||| ||||||||||||||||||| || || ||||| || |||||||||||||||||||| ||| | || | ||||| | | | || | ||| || ||| ||| ||||| ||||||||
GGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCGgtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttca----catgcttctttagtttctttcttcccttttaaagtttaaatgtgcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G28980.1 (Glycine max), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag------------------------
||||||||||||||||| || || ||||| || |||||||||||||||||||| ||| | || | ||||| | | | || | ||| || ||| ||| ||||| ||||||||
----------------------------------------ATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCGgtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttca----catgcttctttagtttctttcttcccttttaaagtttaaatgtgcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgta-gttgtgtcatggccataattcttgagtttcttgtag-------------------------
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----------------------------------------ATGCAAGAGGTTGCAGGGGAACGTGGAGGTTACCTTCATGGACGAGGCGgtactg-tctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S88_45V6.1 (Physcomitrella patens), 5'ss of exon 4
-----------GGATAACGGCCCCGCC--ACATTTTC-TGGTTATTGCA-TATAGATGCAA-GAGGTTGCTGGT----GAAC---GTGGAGGCTATCTTCATGGA--CGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag------------------
| | | | | | || ||| |||| | | || || | || | ||| | | ||| | || ||| || || || || || | | | | ||| | ||| | | | | || ||| || || | | |||| | | | |
ATGCAGGAGGTAGCTGGTGAACGTGGTGGATATCTTCATGGTCGTGGAGgtacagctcaaacaaagtttatatttacggaatcgagcaatggttatatttatagagatgaatttctatagagttgacgttgatgcttgtcatgtggactctattatgatgcttgtcatgtgttgattatcactgttgatatcatattggcattgataaaatgtgcag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatct---ctctctctctctttttttgtttttcgttcttcttt-tgtagttgtgtcatggccataattcttgagtttcttgtag----------------------------------------------------------
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----------------------------------------ATGCAGGAGGTAGCTGGTGAACGTGGTGGATATCTGCATGGTCGAGGAGgtacagctcaaaacgctatttttagcacattgatatcctatgtactgcatgctgatgtttgatgcatgcagtgaa-gactccattgtgatggcggagtgtgttaattatcattgctgacctcttaatgcaattcatgaaatgcacag
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ15111 (Selaginella moellendorffii), 5'ss of exon 3
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtag----ttgtgtcatggccataattcttgagtttcttgtag--------------
||||||||||| || || ||||| ||||| ||| | ||||||||||||||||| ||| || || ||||| || | | |||| | | | | || | | | || | | || | | |
----------------------------------------ATGCAAGAGGTAGCAGGGGAACGCGGAGGGTATTTGCATGGACGAGGCGgtactgttct---tcacttagtttttgaattccttgcatttctctaggaaaagctcgttttttttcttggttttctcacgttttcctgggaggttctttgcagMapped 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|116453294|gb|EG495886.1|EG495886EST: GATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG CTTTAGATAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGG
genomic: GATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatct ... tttcttgtagCTTTAGATAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCGgtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtag
- - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA