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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggctaaacttctccctttcaaatgccacttattagcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA

Basic information

species Glycine max
transcript GLYMA10G30970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
gaggctaaacttctccctttcaaatgccacttattagcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttttgac-cagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
         |  |   ||  ||| | ||     | | ||| | ||  ||| | |     |        | | | ||  |||  ||    |||   |  ||||| || || |||||||||||||||||||||||||| || |||||||||||||| || || |||||||| |||||||| ||||| |||||||| || ||||
------gtgccccatgctcacaattacc-----tgacctttttatttttcttaccaagtgaattgatttatcagtt--attcttgccttgttggaattcagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA

upper sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112240_T01 (Zea mays), 3'ss of exon 2
gaggctaaacttctccctttcaaatgccacttattagcttatgatgcttcattcttta-cgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
|  | |    |  |     |   |  | |||||||| ||||| |  || ||   | || |  |  |  | |||   |     | ||||||  ||    ||||| || || ||||| |||||||| || |||| ||| || || ||||||||||||||||| ||||| || |||||||| || ||||| ||||| || ||||
gttgttgtgttcttaaagatgtgac-ctacttattaccttataa-actacaaagtgtatcaatagtttacttatgcttttgcattgttgaaatt----cagGTTGTCGAAGATGGATACGAGTTTTTCGCTAGCCGTCAACTCGTAACAATATTTTCAGCCCCTAACTACTGTGGAGAATTCGACAACGCTGGTGCCATGA

upper sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
gaggctaaacttctccctttcaaatgcca----cttattagcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttt-tgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
      | | ||  |  |     |||  |    ||||||| ||||| |  | | |    ||   ||  | |||  |  ||    |||  |  | ||  |   ||||| || |||||||| || || |||||||| |||||||| |||||||| |||||||| || |||||||||||||| |||||||| |||||||| || ||||
--cataagatttgactgtaatggatgtgaggagcttatta-cttattactcattaggacttcaatt--ttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA

upper sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
lower sequence: EDO97337 (Chlamydomonas reinhardtii), 3'ss of exon 4
-----------------------------------------------------------------gaggctaaacttctccc-tttcaaatgccacttattagcttatga-tgcttcattctttacgttcct--gcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
                                                                 | | |      |  ||   | |    | |   | |   |   |   |||   |        | ||||  | | ||   |||  ||    |   || |||   ||||||||||||| |||||||||||||| || || || |||||||| || ||||| || || || || || || || ||||| || ||||| || || ||||
gtgcgggtcgtcgcctaggtgttccgcgggtttatggggttggcggaacacgcatcgcatgtcaagggacggggggtacccgactccgggggtcttgtgtggtcccgtatctgcccgaagtgcagagctcctctgaactttgcttgtcttg-catgtggtattg--tagGTGGTGGAGGAGGGGTACGAGTTCTTCGCAAAGCGCCAGCTTGTGACCATATTCTCGGCGCCGAACTACTGCGGCGAGTTCGAGAATGCGGGAGCGATGA

upper sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
gaggctaaacttctccctttcaaatgccacttattagcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
                       |||   ||  | || |  |  |   || ||  ||     ||    |      || | |||   | |        ||||||||||| || || |||||||| || || ||| | || ||||| || |||||||| ||||| || |||||||| ||||| |||||| | ||||||||||
---------------------gtatgatgctcgtgagttctttctttctcgttgctttgagccccatgtc-----tgcaataacaataa--------cagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

upper sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
gaggctaaacttctccctttcaaatgccacttatta-gcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
                               ||| | |||  |||   ||| |||||||  ||  ||| ||| |     ||   ||          | ||||||||||| || || |||||||| || || ||| | || ||||| || |||||||| ||||| || |||||||| ||||| |||||| | ||||||||||
------------------------------gtatgatgctcgtga--gttctttcttta--ttgttgc-tttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

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|208066312|gb|GD865971.1|GD865971
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|14259266|gb|BG882174.1|BG882174
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207704952|gb|GD686383.1|GD686383
EST:     AGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: AGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|18735364|gb|BM528723.1|BM528723
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGGACGAGTTCTTTGCTAACCGGCAGCTTGTAACA-TA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207715220|gb|GD696096.1|GD696096
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|193725684|gb|FK657654.1|FK657654
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208042374|gb|GD838322.1|GD838322
EST:     TTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: TTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208172151|gb|GD970630.1|GD970630
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208122581|gb|GD923161.1|GD923161
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTG
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTG
EST: gi|208168365|gb|GD966885.1|GD966885
EST:     GAGTTTCTTTCTAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: GAGTTTC-TTC-AGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208337465|gb|GE133475.1|GE133475
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207741329|gb|GD717185.1|GD717185
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|193551022|gb|FK506029.1|FK506029
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|193562108|gb|FK516917.1|FK516917
EST:     TTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: TTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207706433|gb|GD687933.1|GD687933
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|193712043|gb|FK647918.1|FK647918
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATG
genomic: CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATG
EST: gi|207735128|gb|GD712911.1|GD712911
EST:     TCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: TCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|193316127|gb|FK282221.1|FK282221
EST:     GAGTTTCTTTCTAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: GAGTTTC-TTC-AGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcattctttacgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA
                                gattaat  putative branch site (score: 3)
                      atttaaattggattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggctaaacttctccctttcaaatgccacttattagcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- -gctaaac
- - - - - ttctccc
- - - - - - - - - - - - tgccact
- - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgag