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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaggtactattgttatgttgcaaagtcagtattcttgtcattggtctgtgttccttttggccttgacatgctatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC

Basic information

species Glycine max
transcript GLYMA09G29970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------tgtaggtactattgttatgttgcaa-agtcagtatt---cttgtcattggtctgtgttccttt---tggccttgac-atgctatctgaacccatgttttgttgct----------cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
                                      | |  || |  ||||  |      | | |  ||||    ||||   || |  | ||||  |||   |  |  | || ||  | | | |  ||||  | |  ||||          ||||||||| ||||| || ||||| ||||||||||||||| | || |||||  | ||||| || || |||||||| || |||||||| || || ||||| || 
gtgctctttttctggtccttaattacttggcatttctttattagttcatttgtattaaaatgatacttggtatcatgcttggtgtttgcgtttgttaatttgtttatctctaacgatattttttaactccattatatcctgctgacaatataacagAACTGGTTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAACTCTGTCATTGCTGGACGTTACCATGTCACAGAATATCTGGGTTCAGCAGCATTCAGT

upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------tgtaggtactattgttatgttgcaaagtcagtattcttgtcattggtctgtgttccttttggccttgacatgctatctgaacccatgttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
                                                                         ||  || | |  || |||  |   ||    | | | |    |   | || ||  |    |   |   ||    ||| |  || | |  ||||  |   ||||||||||||||| || ||||| ||||||||||||||| | ||||||||  | |||||||| ||||||||  | |||||| |||| || ||||| || |||
gtattttctttaaatgattgttccatctgttaatcttgttaaagcataaaaaaatgatatggtaatttccagttatctattgtccttgtgtgcctgtgttcacagtgtggcacctacgccgtatttttaaaagatattttatatcttctaacaccgtctcctgttaattaacagAACTGGCTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGGTCAGCTGCTTTCAGC

upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------tgtaggta-ctattgttatgttgcaaagtcagtattcttgtcattggtctgtgttccttttg---gccttgacatgctatctgaacccatgttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
                                                                  |  || || |||||||  |  ||    | | || |||      | |  ||     | ||||        |    ||   ||| |    || |  | ||  |   ||||||||||||||| || ||||| || |||||||||||| | ||||||||  | |||||||| ||||||||  | |||||| |||| || |||||||| |||
gtaatgcatttaaatgtttgtcccatattttaatcttactaaagcataaaaaatgatgtggtgattttcagttatctattgtccttgtgt---gcctgtgttcacagtgtggcacttaaacctttttataaagtattttgtgtattctaacattatctcctattaattatcagAACTGGCTTTGAAGAAGACAAAAACTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGTTCAGCTGCATTCAGC

upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------tgtag-gtactattgttatgttgcaaagtcagtattcttgtcattggtct-gtgttccttttggcc-ttgacatgctatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
                                           |||   ||||   | || | | | |  |  |  |    ||||     ||| |||  || |  ||   || |  || |   |  |    | || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| ||||||||  | ||||| || || |||||||||||| |||| ||||| || || ||||||
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC

upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
tgtaggtactattgttatgttgcaaagt----cagtattcttgtcattggt--ctgtgttccttttggccttgacatgct-atctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
        | | | | | |||   || |    ||  | | ||| ||||||   || || |  || |  |    |  | || |||| ||    |||||||| |  ||||||||| |||||||||||||| || |||||||||||||||||||| ||  ||||||||||||||||||| || |||||||| || || |||||||| |||
-------gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC

upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 10
tgtaggtactattgttatgttgcaaagtcagtattcttgt-cattggtctgtgttccttttggccttgacatg--ctatctgaaccca--tgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
      ||   ||||  |   | ||       || ||  |  |||||  | | ||   ||||   | |  | |  | | ||||  |||   | || | |    || ||||| ||||||||||||||  | || |  |||||  | ||| | ||  | ||||| ||||||||||| || ||||||||||| |||||||| || |||
-----ttatcgttgtattaagggaaccctgcaatgctcatgtattggattctttttggtttgttgtagttacggtccacctgataccaatcgcttgggtttgtagGACTGGATTTGAGGAGGACAAAGACTTTCCAGTTGTAATTAATGCAGTTGTTGCTGGTCGCTATCATGTGACGGAGTATCTGGGTTCTGCTGCCTTCAGC

upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 3
tgtaggtactattgtt-atgttgcaaagtcagtattct----tgtcattggtctgtgttccttttggccttgacatgctatctgaaccca--tgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
       ||| |||   | |||  || | || | ||||    | |  | | | | | |  ||  | |   |  ||    |  | |  ||   ||  | | |   ||| ||||| |||||||| |||||  | || |  |||||  | ||| | ||  | ||||| ||||||||||| || ||||||||||| |||||||| || |||
-------acttttgacgaggttttaagggcacttttctgtactctactggatttttttagctagtcgttgtttcagttcacataatgccgagtgcctggatttgcagGACTGGGTTTGAGGAAGACAAAGACTTTCCAGTTGTAATTAATGCAGTTGTTGCTGGTCGCTATCATGTGACGGAGTATCTGGGTTCTGCTGCCTTCAGC

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|208038212|gb|GD837052.1|GD837052
EST:     GAGGAGGAATTTGAAACCTTCAATCTAAAGATTGTGCACAGGAAAAACAG                         AACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACT
genomic: GAGGAGGAATTTGAAACCTTCAATCTAAAGATTGTGCACAGGAAAAACAGgcatgtctta ... tgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACT
EST: gi|193642373|gb|FK587247.1|FK587247
EST:     GAGGAGGAATTTGAAACCTTCAATCTAAAGATTGTGCACAGGAAAAACAG                         AACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAA
genomic: GAGGAGGAATTTGAAACCTTCAATCTAAAGATTGTGCACAGGAAAAACAGgcatgtctta ... tgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgtgttccttttggccttgacatgctatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
                 ccttgac  putative branch site (score: 4)
                                          ttttgtt  putative PPT
                                       atgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaggtactattgttatgttgcaaagtcagtattcttgtcattggtctgtgttccttttggccttgacatgctatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - -cttgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt