Sequence
atgc intronic sequence ATGC exonic sequencegtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------gtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
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gtaagtttgttctttagaatctttcaccaataatttcttatcacaaacatgatacatatttaaatgttgggctttttcaaacttcattatt-gtgattcatcttttctactatctggcagATGCTAAAGTTCAAAGATAACAATATTAACAATGAGGGAATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 4
gtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
||||| || |||| | || | ||| | | | ||||||| || | | | | || ||| |||||||| || | | ||| | ||||| | ||| | ||| | || ||| | |||||||||||||| ||||| ||||||||||| |||||| | |
gtaagccttttgt-cttgattcttttgtaagttgccctgaa--attctttaatctaacccatctctact-----gtttggcagATGCTAAATTTCAAGGATAACAATATAAACAATGATGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
---------------gtaaggaagttacacttggtgtttgtacaa-gagaacgtatattattctttcatttgctaattgtattcttgga--aatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
|| | ||| | ||| | || | || | || ||| ||||||| | || | || | || |||||||| || | | | || | || || || | ||||| || |||||||| | |||||||| || ||||||||||||||||||| ||||||| | |
tcttttcaagaccatgtttgacagtgttagttgtttggtgcattctgattatttaaatt-cactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
----------------gtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaat---ttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
| | |||| || || | | || | || ||| ||||||| | | | | || | || |||||||| || | | | |||||| || || || | ||||| || |||||||| | |||||||| |||||||||||||||||||||| |||||| | |
attttcaagaccatgtttgacagtgttagttttttggtgcattcg-gattatttaaatt-cactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 4
----gtaaggaagtta--cacttggtgt-ttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaat----------ttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
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acttttaatggtgctggttgtttgatatattccatttatctagatttgcttgtatttcatggataaatcattatcttaacattccagtttgcattgccagATGCTTAACTTTTCAAACAATAATCTAAACAATGAAGGAAGGTTGCGGACAGTGCTTGATGTTGGTTGTGGTGTTGCAAGTTTTGGAGCATATCTTCTAT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 3
------------------------------gtaaggaagttac----acttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttgga-aatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
||| | | || || | | || | || | | | || | | ||| | || ||||| || | || |||||||| |||| ||| ||||| || | ||||| | ||||| || | | ||||| |||||||| ||||||||||| || |||||||| |||||| | |
gtaagctagttactcctatctagtttggcactaaaataatcaccaaaacataaaactcttatatgac--tggaaaaagttgtaac-tttattgtttatattcatgattggtattacagATGCTCAACTTTCCAAACAATGTCATAAACAATGAAGGAAGACTTCGCAATGTTTTTGATGTTGGCTGTGGTGTTGCAAGCTTTGGAGGATATCTTCTTT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 3
------------------------------gtaaggaagttac----acttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttgga-aatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
||| | | || || || | || | || | | | | | |||| || ||||| || | ||||||||||| |||| ||| ||||| ||| | ||||| | ||||| || | | ||||| |||||||| ||||||||||| || |||||||| |||||| | |
gtaagctagttactcctatccggtatggcactaaaataatcaccaaaacatgaaactcttatatga---ctggaaaaagttataagtttgtagtttatattcatgattggtatttcagATGCTCAACTTTCCAAACAATGTGATTAACAATGAAGGAAGACTTCGCAATGTTTTTGATGTTGGCTGTGGTGTTGCAAGCTTTGGAGGATATCTTCTTT
upper sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 4
---gtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatt------------tgctaattgtattcttggaaattttt--cagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
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atttcattttagggatttctggttctttggtaaattattttagtattttcttctactgcatggttgaagcaataattctatttgtggcttgtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACTGTTTTTGATGTTGGCTGTGGTGTTGCAAGTTTTGGAGCCTATCTTCTTTMapped 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|86064589|gb|DR360346.1|DR360346EST: CATTATGGTGCTGATAAGTATATTGCATCGATGGCAAAT ATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACG
genomic: CATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagt ... aatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
tgctaat putative branch site (score: 2)
tttttc putative PPT
tatattattctttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG