Sequence
atgc intronic sequence ATGC exonic sequencegttagtttatacagacaatggtgtccatctttgttcggttgatgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G17730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------gttagtttatacagacaatggtgtccatctttgttcggttg---atgagttatc-tattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
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gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 4
------------------gttagtttatacagacaatggtgtccatctttgttcggttgatgagtt--atctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
|| ||||| ||| | || | | | | | || | || | || | | || || | | ||||| || || || || | || || ||||||||||| |||||||||||| ||||||||||||| |||||||| || |||||||| || ||||||||||| ||
aagtagatgaacaactgaattcatttatgttatcaaaattttcaaattctccacattgcattattttagtaccttagctattgcattattcat-gctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATTATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAA
upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 4
------------------gttagtttatacagacaatggtgtccatctttgttcggttgatgagtt--atctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
|| ||||| || | || | | | | | || | || || | | || || | | ||||| || || || || | || || ||||||||||| |||||||||||| | ||||||||||| |||||||| || |||||||| |||||||||||||| ||
aagtagatgaacaactgaattcatttatgttattaaaattttcaaattctccacattgcattatttcagcaccttagctattgcattattcat-gctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAA
upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 4
--------------gttagtttatacagacaatggtgtccatc---tttgttcggttga--tgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
|| | | | | | || | ||| |||| | ||| | |||| | | || || | || || |||||| ||| | || | || || ||||||||||| |||||||||||| | ||||| |||||||| ||||| || |||||||||||| ||||||||| ||
ctgtacatgcatttgtaataccagatatagaagactacttatcaaatttgaccatttgcattattttatttcctaatctcttgcattattgatgccacagACAGGAAGTATTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGACGAAAGAGATCAAGGTATTCAAGAAATTCAGTCGCAAATTGGTGAA
upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 4
--------------gttagtttatacagacaatggtgtccatc---tttgttcggttga--tgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
|| | | | | | || | ||| || | | ||| | ||||| | | || || | || || |||||| || | || | || || ||||||||| | |||||||||||| | |||||||||||||||||||| || |||||||| ||| ||| ||||| ||
ctgaacatgcatttgtaataccagatatagaagactacttatcaaattcgaccatttgcattatgttatttcctaatctcttgcattattgatgccacagACAGGAGGTATTATTCTTAGATAATGAGATTTCCTTCAATGAGGCTATCATTGAGGAAAGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAA
upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 4
---------------gttagtttatacagacaat-ggtgtccatctttg-ttcggttgatgagttatctat--tgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
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aaactgggcacatgccctacattatatcatttctaggcattaagaataggttcttctaatatgctctctcccctaaactattagatgatttgtgctgcagACAGGAGGTCTTGTTGTTGGACAATGAGATTGTCTTCAATGAGGCTATCATTGAAGAAAGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGMapped 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|164051155|gb|ES145234.1|ES145234EST: AATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTGGAATCAAAAAG ACAAGAACTTGTACTGTTGGACAA
genomic: AATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTGGAATCAAAAAGgttagtttat ... tttgttgcagACAAGAACTTGTACTGTTGGACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctttgttcggttgatgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
tattgat putative branch site (score: 3)
ttgtttttt putative PPT
ttatctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttatacagacaatggtgtccatctttgttcggttgatgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA