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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccctttactggattaagcatgcatattaattttcttctctaattgctttattgtggtttcttgagtttttttggatcttatccatgttttctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCACAGCCTGAACGCCCACCGCGCCCACCACAATCCTTTAGAGTCTATGTTG

Basic information

species Glycine max
transcript GLYMA17G13470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g09680.t01 (Vitis vinifera), 3'ss of exon 2
---------gccctttactgg-attaagcatgcatattaattttcttctctaattgctttattgtggtttcttgagtttttttggatcttatccatgttttctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCACAGCCTGAACGCCCACCGCGCCCACCACAATCC---TTTAGAGTCTATGTTG
          | || | ||   |||| |||| |||   | || |   ||| ||    || ||   | |||  ||| || ||   ||| |      ||| |  ||  ||||||| || |||||||  | |||||||| || ||||||||||||  |||| ||||||| |||||||| || |||       || |    |||||| | ||||   
ttcaaaatctctctatgcttccattatgcatacatgc-atttatgagctcaaaaaagttaat---gattttatgaattgttcatgatttc-----tgtatcttg-aacagGAATTAGATGGAAGGCTCTTGACTGTAAACAAGGCTGCTCCACGAGGATCACAGCCAGAACGCCCCCCTCGCGTGTTTGAACCTGCTTTTAGAATGTATG---
















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|10847879|gb|BF070480.1|BF070480
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|26058596|gb|CA801510.1|CA801510
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|31465587|gb|CD407615.1|CD407615
EST:     GAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: GAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|5057309|gb|AI735785.1|AI735785
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|6071786|gb|AW101173.1|AW101173
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|31562008|gb|CD487846.1|CD487846
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGA
EST: gi|26058595|gb|CA801509.1|CA801509
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|17400637|gb|BM177419.1|BM177419
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|120530752|gb|EH258885.1|EH258885
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|15203609|gb|BI426377.1|BI426377
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|193693517|gb|FK631643.1|FK631643
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|120534064|gb|EH262197.1|EH262197
EST:     TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
EST: gi|31467356|gb|CD409384.1|CD409384
EST:     TGAGTACCATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTAT                         GAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA
genomic: TGAGTACAATCGAAGAGCTTGAGAAGGCTGTCAAGATGTTCAGTGGTTATgtaagttgtt ... tctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttattgtggtttcttgagtttttttggatcttatccatgttttctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCACAGCCTGAACGCCCACCGCGCCCACCACAATCCTTTAGAGTCTATGTTG
                                        tgttttct  CT-rich tract
                   agttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccctttactggattaagcatgcatattaattttcttctctaattgctttattgtggtttcttgagtttttttggatcttatccatgttttctgtgacagGAACTAAATGGAAGAGTGTTGACTGTTAATAAGGCTGCTCCAAAAGGAGCACAGCCTGAACGCCCACCGCGCCCACCACAATCCTTTAGAGTCTATGTTG

-cccttta
- - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - tgcttta
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt