Sequence
atgc intronic sequence ATGC exonic sequencegttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G17150.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 5
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacat----ttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
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------------------------------------------------------------------ctttgagttcatgtcatgtataagatgtcttaaatatgtgatctttgcgtaacggatccatcccaattcattcgttgttttgtgaact---aatgtaata--cagCCTACTCTATGGAGCAGAAGATTCCTCGATTGCTGGAATGGTATTGGATAGTGCTTTCACTAACTTATATGGCTTGATGATGGAGCTTGTGGATGTCTAC
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 6
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
||| | ||| | | | || || ||| | | | | | | | | | | || | ||||| | | |||| || | || |||||||| |||||||| ||||| ||||| |||||||||||||| | || ||||| ||||||||||||| ||||||||||||||| || | ||||||||
-----------------------------------------------------gttaaaatatctctcatctgttccatatgtgt-tattgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttctttggtgcgg-------------tgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTAT
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagct-ttctaaaggtcta-tgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
|| | | || | || || ||||| || || | || | | | | | | | | | | | ||||| | | |||| || | || |||||||| |||||||| ||||| ||||| |||||||||||||| | || ||||| ||||||||||||| |||||| |||||||| || | ||||||||
-------------------------------------------------------tgttaaaatatacctcatctattctatgtgtgtaattataagtcacatatatgagaatctctagtatagttat-ttctcactttgctttggtgcgg-------------tgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
|| | ||| || | | | || | || || | | || ||||| | ||| | | ||| | | | | |||| || ||||| |||||||| ||||| ||||| |||||||||||||| | || ||||| ||||| ||||||| |||||| |||||||| || |||||||| ||
------------------------------------------------------------atggtcctacctttactccgtatataagtaatt--attagccacccatatattcaaatttc---tagtttaattgactattcccttttactttggtgtgatgt--agTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
|| | | ||| ||| | | | || | | | | || | | | | || ||| | ||| | | | | |||| || ||||| |||||||| ||||| ||||| |||||||||||||| | || ||||| ||||| ||||||| |||||| |||||||| || |||||||| ||
------------------------------------------------------------atggtcttacctttactctgtatacatgtaattatgagccacccttatattcacaactctagtttaattgtctattcccttttactttg-----gtgtgatgt--agTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ08928 (Selaginella moellendorffii), 3'ss of exon 5
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
| | | | ||| | | | |||| ||| | ||||||| ||| ||||||||||| ||||||| || || ||||| ||||| || || ||| ||||||| ||||| ||||| || ||| | || || || || || |||
-----------------------------------------------------------------------------------------------------------gtttgtaaaagcacggtttgctgacaagttggattgacttgcttggatattgttgtgcagTCTTTTCTATGGAGCACAAGATCCATCCATCGCTGGGATGGTTCTGGATAGTCCATTTTCCAACTTGTTTGAGCTTATGCTAGAGCTTGTAGACGTGTAC
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ29782 (Selaginella moellendorffii), 3'ss of exon 5
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
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-----------------------------------------------------------------------------------------------------------gtttgtaaaagcacggtttgctgacaagttggattgactttcttggatattgttgtgcagTCTTTTCTATGGAGCACAAGATCCATCCATCGCTGGGATGGTTCTGGATAGTCCATTTTCCAACTTGTTTGAGCTTATGCTAGAGCTTGTAGACGTGTACMapped 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|19878908|gb|AU239739.1|AU239739EST: AAGTATCCCGTATTGGACTTTGGGGGACGATCTATGGGTGCAGTTACCAG CCTTCTTTATGGAGCAG
genomic: AAGTATCCCGTATTGGACTTTGGGG-ACGATCTATGGGTGCAGTTACCAGgttacttctt ... taatgtgcagCCTTCTCTATGGAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
atttgat putative branch site (score: 5)
aatataatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA