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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacatgttctttgaatcttttgaaagttctgaaggttaaaggaagtcatgaccttattgatgttagcctttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAAAAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT

Basic information

species Glycine max
transcript GLYMA12G03660.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 7
---------gtacatacatgtt-ctttgaatcttt--tgaaagttctgaaggttaaaggaagtcatgaccttattg-atgttagcctttgta-tacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAA---AAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT
             || |||||| ||  ||||| ||  | | |  | ||    |||     | |  | ||  |  |   ||||  || ||||| ||||||| ||||||||||| |||||||||||||| ||||| ||||||||||| ||||| ||||||||   ||||||||||||||  || || || ||||| || |   
gttggtatatcttattcatgttactgagaatcgttactcagaagtttgtca-ttaccttcattattaactgtgatatgtgttcccccttgtaatacagAACGTGAAGGCTGTCTTTGATGCGGCCATTAAGGTGGTTCTCCAGCCACCAAAGCAGAAGAAGAGAAAGAAGAGAAAGGCACAGAAAGCTTGTTCTATAT---

upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------------------------gtacatacatgttctttga-----atcttttgaaagttctgaaggttaaaggaagtcatgaccttattgatgttagcctttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAAAAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT--
                                                                                                |  |||  |||    | |      |   | || |     | | || |  | ||  |      ||||| || |     |  | ||| ||||||||||| || ||||||||||| ||||||||||| ||||| ||||| || || |||||||| ||||||| |||    ||||||  ||||   ||| | |  
gtaaacgcttgaattcaattgtggcttctatgctcaatgtgatgtgttggctctgctttaaacaattatgtaacttttccctttgtattctagcttgcgcatctatgaagatgggtggccagagtatgtagtccatcatggctgcaagatttttgtgtcttat-gacgcctttcggtctatgcagAATGTGAAAGCAGTTTTTGATGCTGCCATCAAGGTTGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAGAAAAA---ACAAAAGAACTGTGTTATTCTCTGA

upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
-----gtacata-catgttctttgaatcttttgaaagttc-------tgaaggttaaaggaagtcatgaccttattg-atgtta--gcctttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAAAAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT--
       || |  |||     | | |  | | ||   |||       ||  | |||||  |   |   | ||| |     |||   | ||||   | ||||||||||| || ||||||||||| || |||||||| ||||| ||||| || || |||||||| ||||| | |||    ||||||  ||||  |||  | |  
ggtcacaacgtgtcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAAAA---ACAAAAGAACTGTGTCATACTCTGA

upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtacatacatgttctttgaatcttttgaaagttctgaaggttaaaggaagtcatgaccttattgatgttagcct-ttgtat------acagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAAAAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT---
         ||    || ||  |   || | | |  |   |   |     |     || |  |    |  ||||||      | ||||||       ||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| || || ||||||||   ||||| ||||  |||||||  ||||  |||| | |   
tttctgtaggtgggaacttgcaccaagattatgtcaactatgtagtgcactgtgtcaattatttttttgtttgatggcgatttattgtattctattgcagAATGTGAAAGCAGTTTTTGATGCCGCCATAAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAA---GAAGAAAAAGAAGCAAAAGAACTGTGTCATTCTCTAAT

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|208044920|gb|GD840154.1|GD840154
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|298171505|gb|HO016537.1|HO016537
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|192329145|gb|FK021132.1|FK021132
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCCCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|193463924|gb|FK427848.1|FK427848
EST:     TTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: TTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|58014286|gb|CX701028.1|CX701028
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|58020948|gb|CX707690.1|CX707690
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|151401174|gb|EV270988.1|EV270988
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAA-CGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGG
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGG
EST: gi|151405308|gb|EV275122.1|EV275122
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|18039985|gb|BM308279.1|BM308279
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|308222701|gb|HO760611.1|HO760611
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|58021197|gb|CX707939.1|CX707939
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|192329144|gb|FK021131.1|FK021131
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCCCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAGgtacatacat ... ttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctgaaggttaaaggaagtcatgaccttattgatgttagcctttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAAAAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT
                              tattgat  putative branch site (score: 3)
                                          cctttgt  putative PPT
                             ttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacatgttctttgaatcttttgaaagttctgaaggttaaaggaagtcatgaccttattgatgttagcctttgtatacagAATGTGAAGGCTGTTTTTGATGCGGCCATCAAGGTAGTTCTCCAGCCCCCAAAACAGAAGAAAAAGAAGAGAAAGGGGCAAAAGGCCTGTTCCATTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA