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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatggctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG

Basic information

species Arabidopsis thaliana
transcript AT1G07110.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 15
gtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatg-gctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgtta--ttcta-cttttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG
|| | | | | || | || || | | || || | | || | || || || | || | || |||| |||||| | ||||||||||||| ||||||||||||||||| ||||||| |||||||||
---------------------------tagagtacctgtgtgtgtgtgtccttgaattttgctctaccca---tttagtttcaagtgactttgattgctaattgttaatagcttctgtcttttggtctagGTGAACAATATCAGTGGTTACCTTCCTGGACGAATTGTCTTTTTCTTG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 20
gtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatggctatttcatctagtc--ttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG
|||| | | | | | || | | | | ||| |||| | ||| | | | || ||||| | | |||||| || || | | |||||| | ||||||||||||| ||||| ||||||||||| ||||||| |||||||||
-------------------tgtagagt-acctgtgtgtgtgtccttgaattttgctctacccatttagtttcaa-gtgac-tttgattgct--aactgttaatagcttctgt----cttttggtctagGTGAACAATATCAGTGGCTACCTTCCTGGACGAATTGTCTTTTTCTTG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 16
gtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatggctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG
||| | | | || | || || | | | | ||| | | | | ||||| ||| | || | || ||| | | |||||| | ||||||| ||||| ||||||||||||||||| ||||||| |||||||||
--------------------gtagagt-acatgtgtgtgtccttgaattttgccctactcatttattttcaagtgtgactttgatttgtt-aattgctaataacttctgt----cttttggtctagGTGAATAATATCAGTGGTTACCTTCCTGGCCGAATTGTCTTTTTCTTG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------gtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatggctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttg-ttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG
| | || | | | | | | || | | | || | |||| | | || | ||| | | |||| | ||| ||||| | | | | ||| ||||||||| |||||||||||||||||||| ||||||| ||||| ||
gtgagtaaattcagtttgccaagcaagtaattcaagtatttagaggtaccaatagcaatcgatactact-tctcatttgaggtgaag-aaagtataggaggtgatgagaaaatgagtttttgacttaattgttggctgcgcttgtagGTGAACAGCATTAGTGGTTACCTTCCTGGTCGAATTGTGTTTTTTCTG

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|164116556|gb|ES087977.1|ES087977
EST:     GTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA                         GTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTC
genomic: GTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAAgtacgtctct ... tttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG
       acttgat  putative branch site (score: 5)
 ttctactttt  putative PPT
 ttattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatggctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcagGTGAACAATATTAGTGGTTACCTTCCTGGGAGAATTGTATTTTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA