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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatattcaaactttttctgcttaccaaaacttaaggatataatgatgaacattggaaaattattttcagatatatgattttcacacaattattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT

Basic information

species Glycine max
transcript GLYMA09G32900.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G700662_T01 (Zea mays), 3'ss of exon 7
----------------ccatattcaaactttttctgcttaccaaaacttaaggatata-atgatgaacattggaaaattattttcagat-atatgattttcacacaattattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT
                |         |  ||||  |    |||| |    | |   || || ||  |          || |||  |  | || |||| || |  |||     | |||||    ||  | |||||||||   |||||  | ||||| ||||  || || |||||||| |||||||||||||||||| |  ||||||||||  | || ||
gtgatcttcacatgggcggagggagtatcttttagggactccaatagaagaaggcttatatcatataggaattgtggttgtttctatcttatttgatgtttattcaaac---taacagGTCGATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: GLYMA09G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G314386_T01 (Zea mays), 3'ss of exon 4
ccatattcaaactttttctgcttaccaaaacttaaggatataatgatgaacattggaaaattattttcagatatat-gattttcacacaattat-tttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT
 || ||  |||||| |     ||      |||  |  | |  | |    | |  | ||   |  ||     ||| |  |||       | |||   | |||||  | ||  | |||||||||   |||||  | ||||| |||   || || |||||||| |||||||||||||||||| |  ||||||||||  | || ||
-ca-atgaaaacttatatcttttttagggactccaatagaagaaggcatatacagtaaccgtggttgtttctatcttaattgatgtttatttaaactaacagGTCTATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCCTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: GLYMA09G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G386125_T01 (Zea mays), 3'ss of exon 8
ccatattcaa-actttttctgcttaccaaaacttaaggatata-atgatgaacattggaaaattattttcagat-atatgattttcacacaattattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT
 ||||   |  |  ||||  |    |||| |    | |   || || ||  |          || |||  |  | || |||| || |  |||     | ||||     ||  | |||||||||   |||||  | ||||| ||||  || || |||||||| |||||||||||||||||| |  ||||||||||  | || ||
gcatagggagtatcttttagggactccaatagaagaaggcttatatcatataggaattgtggttgtttctatcttatttgatgtttattcaaac---taacagTTAGATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: GLYMA09G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------ccatattcaaactttttctg--cttaccaa---aacttaaggatataatgatgaacattggaaaattattttcagatat---------atgattttcacacaattatt-ttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT
                                                                  | |  |  | ||| | |||  |||   ||   ||  | ||   | |  ||||| ||  | | |    | |||   | |         ||||   ||||    |  |  ||  ||| || ||  | ||||| ||||  ||||| ||||| ||||| |  ||||| ||||| ||||||||||||||||| ||| |  |||||||||| ||||||||
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT

upper sequence: GLYMA09G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g02260.t01 (Vitis vinifera), 3'ss of exon 4
ccatattcaaactttttctgcttaccaaaacttaaggatataatgatgaacattggaaaattattttcagatatatgatttt-cacac-aattatt--ttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT
     |||||   | |||| |  || ||   |      |  || ||    ||||         ||||| |  ||    || |  | ||    | ||  | ||||| |||||  |  ||||||||| ||||||||||||  |  ||   |||||||||||||||||||||||||||||||||    |||||||||| |||| |||
---ccttcaacactattct-cccacaaagtttaggtcttggaaagagttccatttttcttcctttttcggtcatccatttatataaactggctgttcatgacagGTTTGTCAGTTAATGGTGATTCACAAGGAGTTGATAGAATCCTGGGTGCACTTTCTGCTCATATGTGGCCTGGAATGACCCTGAAATCTGGTGATAAGAT

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|51335725|gb|CO979591.1|CO979591
EST:     CAATATTGAGTTCATTGAGGCATGTGGTTCAAATGCTGATTTTGACAAAT                         GCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCAC
genomic: CAATATTGAGTTCATTGAGGCATGTGGTTCAAATGCTGATTTTGACAAATgtaaaacttc ... tattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCAC
EST: gi|151395592|gb|EV265469.1|EV265469
EST:     CAATATTGAGTTCATTGAGGCATGTGGTTCAAATGCTGATTTTGACAAAT                         GCTTGTCCATAGATGGTGATTTACAAG-AGTTGAGCGTCTCTACAGTGCAC
genomic: CAATATTGAGTTCATTGAGGCATGTGGTTCAAATGCTGATTTTGACAAATgtaaaacttc ... tattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaacattggaaaattattttcagatatatgattttcacacaattattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT
                                            ttatttt  CT-rich tract
           aaaattattttcagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatattcaaactttttctgcttaccaaaacttaaggatataatgatgaacattggaaaattattttcagatatatgattttcacacaattattttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT

- - - tcaaact
- - - - - - - -ttctgct
- - - - - - - - - - - - ccaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacacaa