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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC

Basic information

species Arabidopsis thaliana
transcript AT1G04170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| | | | | |||| || | ||| | | || | | | ||| || || | | | || || |||||| | | | ||||||||||| || || || ||||| ||||||||||||| || || |||||||| ||||| || || || || ||||||||||| || ||||||||||| |||
----------gttgt-tgaactgctcaatcgt--ttttagta-tgtatgtacttcata---tgcaatctgtttatttgttttatatagttctgatttcttccttgtgattt--gtacagACTGTTCGCTTCAAGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGTTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGCCCACGAC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
| | ||| | | || | || | | | || | | || | || || ||| | || ||| | ||| |||||| | | | | |||| || || || || ||||| ||||||||||||| || || |||||||| ||||| || || || || ||||||||||| || |||||||| || |||
---------gttcatgaacatctttcatatttagtatttatg---ttcttcacatgtaa---ttcatatatttatatttgtatagttgtcctgatgtcttccttgtgatttgt----agACCGTTCGCTTCAAGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGCTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGTCCACGAC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| || | || || || || || || || | ||| ||| || ||| | || | || ||| | | | |||||| | | | || |||||||| ||||| |||||||| ||||||||||||||||| || |||||||| |||||||| || || || ||||| ||||| ||||| ||| || || |
-------ttatacataagcattccatcttt-tattcttaatacacatttt--cttttagctttggat-atttacactgt------tgacctgtgttgtttccgtgaatgtt--gtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatt-tctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| ||| | | || || | || | | | | | | | || || | || || | | | || ||| |||||||| ||||| |||||||| ||||||||||||||||| || |||||||| ||||| || || || || ||||| ||||| ||||| || || || |
--------------------ttacacgtaagcatgccatatattattcttcatacacattctccgttagccttggatatttaaactgttgacctctgttgttttcatgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCTAATGCAAAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaatttgattatgcggttttc-acaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
||| | | | || || || ||||| || || | | | | | | | || || | | | |||| ||| |||||| ||||||||| |||||||||||||| ||||||| || ||||| || || |||||||||||||| || ||||| ||||||||||| ||||| |||||| | |
-----------ttaggagacagtggaccatagtcatcctctag--ttattttgttaagaatatctatatgcttagatctgaaaggtggccctttatgatttgtttatct-------acagACTGTTCGTTTTAAAAATGAGCTGGAGCGAAATATTACTATCAAACTTGGATATGCAAATGCAAAGATATACAAATGTGAAGATGAACGGTGCCCTCGTC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaatttgattatgcggtt-ttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggag-tgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| | | || || || |||||||| | || | | | | ||| || | || | | | | |||||||| |||||| ||||||||| |||||||||||||| ||||||| |||||||| || || |||||||||||||| |||||||| ||||||||||| ||||| |||||| |||
------------tagaagatggttgaccatagtaatcctctaa--ttactttgttaaaaatatttacaggcttaaatctgaaaggtgggtcctttatggtttatttatct-------acagACTGTTCGTTTTAAAAATGAGCTGGAGCGCAACATTACTATCAAACTTGGATATGCAAATGCCAAGATATACAAATGTGAAGATGAACGGTGCCCTCGAC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 1
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaat-tggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
| | | |||||| || | || | |||| | || || | | | | | ||| | || ||||||||||| || || |||||||||||||||||||| || || ||||| || ||||| || || |||||||||| ||||| || ||| ||||||| | |
-----------------------------------------gtgatctagagcttgttttgtgtctccagtgccgagttgatgttgttttctttgtttgattctttgttctgcttctcagACTGTCCGCTTCAAGAATGAATTGGAGCGTAACATCACAATCAAGCTCGGCTATGCGAATGCGAAGATTTACATGTGTGAAGACGAGCGATGCCCTCGGC

upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 1
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttcta-gcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| ||| ||||| | || | | | ||| | | ||| || | | | ||| | || || | ||| || ||||||||||| || || |||||||||||||||||||| || || ||||| || ||||| || || |||||||||| ||||| |||||| ||||||| | |
------------------------------gtgatc-tagagcttgttttgtgtctccagtgccgagt---ttgatgttgtt----ttctttgtttgattctttgttctgcttc--tcagACTGTCCGCTTCAAGAATGAATTGGAGCGTAACATCACAATCAAGCTCGGCTATGCGAATGCGAAGATTTACATGTGTGAAGATGAGCGATGCCCTCGGC

Mapped 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|164146805|gb|ES184847.1|ES184847
EST:     ATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG                         ACTGTACCGTTT-AAAAATGAATTGGAGCGTAACATTACCATTAAG
genomic: ATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttg ... ctctgtacagACTGT-CCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
 gtttgat  putative branch site (score: 5)
 tttccttatcttctct  putative PPT
 atttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG