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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC

Basic information

species Arabidopsis thaliana
transcript AT1G16710.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------------gtaagt-tctggtttttcaacctaggtttatgtggtcttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
                                                                   || | | |||     | |  |   |  |    || || |  |         || |    |  || | |   || ||   | | ||||| || ||||| |||||||| ||| |||| || ||||| || || ||||||||||||||||||||  |||||||||| ||||| ||| ||||||||||||
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcat-tgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatgga-----tgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
                                                                       |   | |  |    |  | |  |     | |  |||||| | ||  |   |     || |    |  || | | |||| |  | | | ||||| || ||||| |||||||| ||  |||| || ||||| || || |||||||||||||| |||||  |||||||||| ||||| ||| ||||||||||||
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcac-cgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------gtaagttctggtttttcaa-cctaggtttatgtggtc-------ttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
                                                                 |  |||   ||  |||||     | ||| | |  |        |||||   || ||  ||  || |   || ||      ||||  | ||| ||||||| || || || || |||||    |||||||| || ||||||||||||||||| ||||| ||| | |||||||| ||||||||  ||||||| ||||
gtaacctttagttctaattccttgtccttgtgttgggtggaatattatacagccttgtggaaccctttgttggagtcattcaagttctgatttgtttccttcctgtagttctattctatataaatagttgagtagtttt-cgttatgattttcttttagATTGGATACCTTGAGTATTGCAAGAAACGTGGTTTTACAAGCTGCTACATATGGGCATGTCCTCCATTAAAGGGTGAAGATTATATTTTATATTGTCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
-------------gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatggatgat--tcaagggtattataccc--------tgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
              |||| ||| | |||  | ||     ||| | | | |||||  |       |  ||  ||  |   ||||||           | ||   |||| ||||||| ||||| ||||| |||||    |||||||| || |||||||| || ||||||||||| ||| | ||||| || ||||||||  ||||||||||||
gtaaatttggacactaagatcttgctttggagcccttcctta-gagatattctagttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 12
-------------gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatggatgat--tcaagggtattataccc--------tgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
               ||| | | | |||   |||     ||| ||| | |||||  ||      || ||  ||  |   |||||            | ||   |||| ||||||| || || ||||| |||||    |||||||| || |||||||| || ||||| ||||| ||| | ||||| || ||||||||  ||||||||||||
gtaaatttggacaccaagatgttgctttggcacccttcctta-gtgatattctagttttgggttattatcttcctgtaaattatgtttgatacaaattatttctttttagATTGGATACCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCCTGTCCTCCATTAAAGGGAGAAGATTATATTTTATATTGCCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 9
------------------gtaagttctggttt-ttcaacctagg---tttatgtggtcttcta-cattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
                    ||  | |  ||| |||    |  |   ||  | |||| |   | | ||  ||    |  |   || |  |||| ||   |   ||| |||||||| ||||| |||||||| ||   ||| |||||||| || ||||| |||||||||||||| ||  |||||||||| || |||||  | ||||||||||
gtgagttttagtattacgccaatcttttatttattcttgatgagcaattcttatggtttggaatctttttatattgggctattggcttatatatccgattctctttccagATTGGATATCTCGAATACTGTAAGAAGCGGGGTTTCACAAGTTGCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 11
----------gtaagttctggtttttcaacctaggtttatgtggt-cttctacattacatggatgattcaagggtattataccctg---atgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
           ||  ||||| |  |  ||| | ||||    || | || ||||  | | |   |    | |    | |  |   ||   || ||| | |||||||| ||| | || || ||      | | ||||| |  || || ||||| |||||||| |||||| | |||||||||||||||||  ||||||| ||||
atttgtgttaatattttctg-taatagaactttggttctgctgctgctgctactgttcttctgtttgcctattaaacttaattgtgtacatacttctgcagATTGGCTATTTAGACTATTGTCGGAGGAGAGGTTTTAGTAGTTGTTACATTTGGGCTTGCCCACCATTAAAGGGTGAGGATTATATTTTATATTGTCATC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S462_17V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
                 |||  | | ||  | |    |  |||  |  | |  | |  | |     ||  | |  |   | ||      |||| || || ||||| || ||||| || |||||      | | ||||| |  ||||| ||||| |||||||| ||||| || ||||| |||||||||||  ||||||| ||||
aattttttttctttacttaaaatgtagtgctgctgtttctgttgttacg-ttgtttgtactg-gcagaccagttgaacttgttggcgtatgat-ctgttgcagATCGGCTATCTAGATTACTGTCGGAGGAGAGGTTTTAGTAGCTGTTACATTTGGGCTTGCCCACCTCTAAAGGGAGAGGATTATATTTTATATTGTCATC

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|116434362|gb|EG476954.1|EG476954
EST:     AGTCTGCTAATGGGGAGGCTCTGCGCACTTTCGTTTACCACGAAATTCTT                         ATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATA
genomic: AGTCTGCTAATGGGGAGGCTCTGCGCACTTTCGTTTACCACGAAATTCTTgtaagttctg ... gctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
                                      ccctgat  putative branch site (score: 4)
                                            tgctttttc  CT-rich tract
                               tattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatggatgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT