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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttagttaaatatcacagttgttgacttcaatatacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA

Basic information

species Glycine max
transcript GLYMA08G12970.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 16
--gtatgtatttagttaaa----tatcacagttgttgacttcaatatacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA
     | || ||||   |     |||||   |  ||||||  ||| |   ||  |||||| |   | | |          ||||||| |     |||||||| ||||| || ||||||||||||||  | ||||||||||||||||| ||||  ||||| || ||    || || || |||     |     |   |
gttggtatacttagcataggtcttatcatgatgtttgactgaaatctgaggc--ccttacgccatttcct----------ttttttttcccttgcagTTTGCCACTGAGGCGGCCATTACTATCCTGAGGATTGATGACATGATCAAACTTACGAAGGAAGAGAGCGGGAACGAAGAGTAACAAGCATTGACACTCA

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 16
-gtatgtatttagttaaatatcacagttgttgacttcaatatacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGATTAA--AGTATAACTGAATCTA
  || |  | | |||   |        || |   |   || |     ||   | |  |      | | |||    |  | || ||    |||||||| || || |||||||||||||||||  | ||||| |||||||||||||||| |||||| |||      || || || |||  ||   | | | |    
gttaggcctcttgtttctttctcgtcatggtatttgtgatgtctgagttttatcccaattccgatcatcta----tcctgttcctgttgcagTTTGCCACGGAGGCTGCCATTACTATCCTGAGGATTGACGACATGATCAAGCTTACCAAGGAAGAAGAGGGTAACGAAGAGTAAGCAGCCCACCAGTAGT--

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtatttagttaaatat-cacagttgttgacttcaat-atacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGA---TTAAAGTATAACTGAATCTA
           || |||  | || |    || |  |  || ||| | |||  || || |   |    ||||  || || |  |       ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||||||| |||| ||||||| ||| ||||| ||   ||| || | | | |  |   
-----------gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagagt-ccagctgaaatttctggtgtg----cagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT---

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 16
------------------------------------------------------------------------------gtatgtatttagttaaatatcacagttgttgacttcaatatacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAG-GATTAAAGTATAACTGAATCTA
                                                                              |    |  ||  ||  || |    |||  |  ||    | |   |     | | |    ||| |||  |   |    | ||  ||   |||||||||||||||||||| ||||| ||||| |||||||||||||||||||| ||  ||||||| |||  |    ||  | ||    | | |  | |||    
gtaagaaacatgtgcttttgaaagattcccttttaatatatgaagattttttgacagatatgtactgtctcgtttctggatcattgttctttgtatgttgaggttaattgctctggtgtgtgggggtgtaagatca-tgcctgatgtgacatcggtatt--ttttgcagTTTGCAACTGAAGCTGCAATTACAATCCTACGAATTGATGACATGATCAAACTGTTCAAGGAGGAAGATGGTGATCGGTGACATCACTTTCGCAGAAGGA-

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|10844852|gb|BF071031.1|BF071031
EST:     TGGAGGCTGGAGTTATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATG
EST: gi|58021211|gb|CX707953.1|CX707953
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|298168848|gb|HO009778.1|HO009778
EST:     TGGAGGCTGGAGTTATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|193682839|gb|FK623867.1|FK623867
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|192311649|gb|FK004868.1|FK004868
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGGTGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|298165014|gb|HO011063.1|HO011063
EST:     TGGAGGCTGGAGTTATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATG
EST: gi|17021742|gb|BM092776.1|BM092776
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|10255075|gb|BE822841.1|BE822841
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|120495038|gb|EH223205.1|EH223205
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|208132784|gb|GD927357.1|GD927357
EST:     TGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|192324297|gb|FK018273.1|FK018273
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCCTTCGAATTTGATGACATGATCA
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCC-TTCGAATT-GATGACATGATCA
EST: gi|58022777|gb|CX709518.1|CX709518
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|208123775|gb|GD922395.1|GD922395
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|208181510|gb|GD974147.1|GD974147
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|58017859|gb|CX704601.1|CX704601
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|51335203|gb|CO979069.1|CO979069
EST:     TGGAGGCTGGAGTTATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|58019703|gb|CX706445.1|CX706445
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
EST: gi|151398434|gb|EV268305.1|EV268305
EST:     TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... acttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA
           tccttac  putative branch site (score: 2)
                                      tttttttacttcccc  putative PPT
                                tagaagttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttagttaaatatcacagttgttgacttcaatatacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT