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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagctatgtcctcccggcttttttcttatttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC

Basic information

species Arabidopsis thaliana
transcript AT3G06550.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 7
gtaagagctatgtcctcccggcttttttcttatttttggctgtcacctacttgaaatt--ctaacata--ttcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
           || |  |            | ||  ||  | ||  | ||| ||  ||  |||||||   |||    || ||||||||||||||| || |||||| | || ||||||| |||||| ||||| |||||   ||| |  || || || || || || |||||||| || || || |
-----------gtgcatctttacaccccactgttcctgattctctac-actagagtttttctaacatggtttcaccttcaacagATGATGTGGCGCCTCAATTTCTTTGTTATATTCTGCTGCATTGTCCTGAACAATGATTATACACTCTATTATATTTGTCCTATGCACACCCTTTTCACCC

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 7
gtaagagctatgtcctcccggctttttt-cttatttttggctgtcacctacttgaaatt-ctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
      || || ||||       |     ||   ||||   | |        || |||  ||   | ||  ||| |   ||||||||||||||||| |||||| | ||  | ||||  || || || || ||||||||||||||| |||||||||||||||| ||||||||||| || ||||
--gtatgcaatttccttgaactataaaagctcgctttttcatatatttggactgtaataactgcaacatatttgttgagcagATGATGTGGCGGCTTAATTTCTTTGTGGTGTTCTGTTGTATTGTACTTAACAACAGTTACATGTTATACTACATCTGCCCCATGCACACTCTTTTCACTC

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 7
gtaagagctatgtcctcccggcttttttctta--tttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
      || || ||||       |      |   |||||     |       |   || |  ||||||||  | |    ||||||||||||||||| |||||| | ||  | |||   || || || || ||||||||||||||| |||||||||||||||| ||||||||||| || ||||
--gtatgcaatttccttgaactataaaagctgactttttaatatttggtctgtactaactgcaacatattggttga--gcagATGATGTGGCGGCTTAATTTCTTTGTGGTGTTCAGTTGTATTGTACTTAACAACAGTTACATGTTATACTACATCTGCCCCATGCACACTCTTTTCACTC

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 7
gtaagagc---tatgtcctcccggcttttttctt--atttttggctgtcacctacttgaaattctaacatattcttggtcta-cagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
||||  ||   ||  ||      | ||  ||| |  | ||    |  | |  | ||     |  ||  |  || || ||  | ||||||||||||||||| |||||| ||||  | || | |||  | ||||| || ||||| || |||||||||||||| ||||| ||||||||||| || ||||
gtaactgcccctaaatctcttaagtttgattcatggagttccatccatgatattctgattctaatagtaagttttttgttgaacagATGATGTGGCGGCTTAATTTCTTGGTGTTGTTTTGCTGTGTTGTCCTTAATAACAGCTATATGCTATACTACATTTGCCCCATGCACACTCTTTTCACTC

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
--------------------------gtaagagctatgtcctcccggcttttttcttatttttg-gctgtcacctacttgaaattctaacatattcttggtct---acagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
                           |   ||   |   | ||  ||  |  ||| ||      |||  |  || |  || |  |     |   ||  |  |    |||||||||||||| || || ||| ||||  | ||| | ||| | || ||||||||||| |||||||| |||||||||||||| ||||||||           
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------gta-agagctatgtcctcccggcttttttcttatttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
                   ||   ||   | ||     |   | ||   |  || | |    ||     | || | |       |    |   |   ||||||||||||||||| |||||||||||| | ||   |||||| || || |||||    |||||||| ||||||||||| |||||||||||||| || ||||
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ29067 (Selaginella moellendorffii), 3'ss of exon 7
gtaagagctatgtcctcccggcttttttcttatttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
                         |  ||  || || ||  ||      |     ||     |    ||||     |||||||||||| |||| || || || || |  || | ||||||||||||||||||||| |||||||| ||||||||||| || ||||| || || || ||  
------------------------gtaactgcttctttgcactcgtaagttcatgctttgtgaacgcacttg-----cagATGATGTGGAGGCTCAACTTTCTTGTGACCTTTTGCTGCATCGTCCTCAACAACAGCTACATGCTCTACTACATCTGTCCTATGCATACCCTCTTCACAT

upper sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ17601 (Selaginella moellendorffii), 3'ss of exon 6
gtaagagctatgtcctcccggcttttttcttatttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
                         |  ||  || || ||  ||      |     ||     |    ||||     |||||||||||| |||| || || || ||||  || | ||||||||||||||||||||| |||||||| ||||||||||| || ||||| || || || ||  
------------------------gtaactgcttctttgcactcgtaagttcatgctttgtgaacgcacttg-----cagATGATGTGGAGGCTCAACTTTCTTGTCACCTTTTGCTGCATCGTCCTCAACAACAGCTACATGCTTTACTACATCTGTCCTATGCATACCCTCTTCACAT

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|125093477|gb|EL151043.1|EL151043
EST:     TTTCTTATTATTACATTCGCAAGGACTTTAGCCTTGCAAGGTTTGCACAG                         ATGATGTGGCGGCTAA
genomic: TTTCTTATTATTACATTCGCAAGGACTTTAGCCTTGCAAGGTTTGCACAGgtaagagcta ... tggtctacagATGATGTGGCGGCTAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttatttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC
                               ttctaac  putative branch site (score: 1)
                                       tattctt  CT-rich tract
                            aaattctaacatatt  TA-rich tract