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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaaattatatgatgatccaggaggaccatggattccatgaaattatatgctctcaaagtatttactatttatctaaacaagtattgtatcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTACAAGCAATTTCTCTACTAGCTCCTGTTCTGGGCTCGGAGATTACTTCTT

Basic information

species Glycine max
transcript GLYMA07G10000.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 10
atgaaattatatgatgatccaggaggaccatggattccatga--aatta--tatgctctcaaagtattt---actatttatctaaacaagtattgtatcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTACAAGCAATTTCTCTACTAGCTCCTGTTCTGGGCTCGGAGATTACTTCTT
       || | || | |   |||  |  ||  | || |||   |||||  |||     || | |  ||   | | ||||| |   ||| | |  | |   ||  |||||||||| | | | |   | ||||||||||||||||||||||| |  || ||||| |||||| | |||||||||||  ||||  | || || || |   
-----ggtaaa-gagggtattggaataaaatttactc-atggttaattaattatatcaacagattgattgaaaatctttatattgtcaaatctcttttatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 11
atgaaattatatgatgatccaggaggaccatggattccatgaaattatatgctctcaaagtatttactatttatctaaacaagtattgtatcctttg-cagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTACAAGCAATTTCTCTACTAGCTCCTGTTCTGGGCTCGGAGATTACTTCTT
 | | | | |    ||     |||     ||  |      |   | | |||||         || | |  |     ||| || |  |  || |  || ||||||||||| ||| |||   | ||||| ||||||||||||||||| ||| | || ||||||||||| || || |||||| ||||| | || ||||| |  |
-taacacttttctttggcaatggaaatgtattaagatatagctgtgacatgctgatttgcctttgaattatggctaaaataactcatcaataccctgacagGTTTTGGATATGATTAACAACCCACACTATCTGTATCGGATGACCATCCTCCATGCAATTTCTCTCCTTGCCCCTGTTATGGGCCCAGAAATTACATGCT
















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|193409043|gb|FK372865.1|FK372865
EST:     TGGCAGAAGAATTTGGACCGGATTGGGCAATGCAGCACATTATTCCCCAG                         GTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTA
genomic: TGGCAGAAGAATTTGGACCGGATTGGGCAATGCAGCACATTATTCCCCAGgtttttatag ... tcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTA
EST: gi|192310534|gb|FG999543.1|FG999543
EST:     TGGCAGAAGAATTTGGACCGGATTGGGCAATGCAGCACATTATTCCCCAG                         GTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTT
genomic: TGGCAGAAGAATTTGGACCGGATTGGGCAATGCAGCACATTATTCCCCAGgtttttatag ... tcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTT
EST: gi|57575814|gb|CX548785.1|CX548785
EST:     TGGCAGAAGAATTTGGACCGGATTGGGCAATGCAGCACATTATTCCCCAG                         GTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTA
genomic: TGGCAGAAGAATTTGGACCGGATTGGGCAATGCAGCACATTATTCCCCAGgtttttatag ... tcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgctctcaaagtatttactatttatctaaacaagtattgtatcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTACAAGCAATTTCTCTACTAGCTCCTGTTCTGGGCTCGGAGATTACTTCTT
                           atctaaa  putative branch site (score: 3)
                                           tatccttt  putative PPT
               tatttactatttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaaattatatgatgatccaggaggaccatggattccatgaaattatatgctctcaaagtatttactatttatctaaacaagtattgtatcctttgcagGTTTTGGACATGGTTACTGATCCACATTATCTGTATCGGATGACAATCTTACAAGCAATTTCTCTACTAGCTCCTGTTCTGGGCTCGGAGATTACTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - -tgatgat
- - - - - - - - - - - - - -ccatgga
- - - - - - - - - - - - - - - - - - ccatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaca