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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttatcttattttttatacttatgtacatagtatgatttatgggaaaacttaagttactaatgcaattttttacattaactgttttcctgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG

Basic information

species Glycine max
transcript GLYMA14G02260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02410.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0090g01020.t01 (Vitis vinifera), 3'ss of exon 6
--tatttatcttattttttatacttatgtacatagtatgatttatgggaaaacttaagttactaatgcaattttttacattaactgttttcctgtgat----gcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG
   | | |    |   |  |  |||||     | ||    | |    |      ||   | | | |     |  || |||| ||  ||| | ||| ||    |||||||||||| |||||||||||  |||||||||||||||||
atcactaaaaccagcatg-aggcttat-----tggttcactatgcatgtgtgtctagtgtgcgatttttcatccttgcattgaccctttacatgttatttgtgcagCCTCTTGTTTCAGGTGCTGCTTTGGGATTGGAAGGGCAG
















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|192312358|gb|FK005362.1|FK005362
EST:     ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAG                         CCTCTTGTATCAG-TGCTGCACTGGGATTGGA
genomic: ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAGgtaaatctta ... tgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGA
EST: gi|208156442|gb|GD957676.1|GD957676
EST:     ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAG                         CCTCTTGTATCAGGTGCTGCACTGGGATTGGGAGGGCAG
genomic: ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAGgtaaatctta ... tgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG
EST: gi|5688245|gb|AI941260.1|AI941260
EST:     ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAG                         CCTCTTGTATCAGGTGCTGCACTGTGATTGGAAGGGCAG
genomic: ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAGgtaaatctta ... tgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG
EST: gi|192312357|gb|FK005361.1|FK005361
EST:     ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAG                         CCTCTTGTATCAG-TGCTGCACTGGGATTGGAAGG-CAG
genomic: ATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAGgtaaatctta ... tgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaacttaagttactaatgcaattttttacattaactgttttcctgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG
                                    ctgttttcct  CT-rich tract
                     aattttttacattaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttatcttattttttatacttatgtacatagtatgatttatgggaaaacttaagttactaatgcaattttttacattaactgttttcctgtgatgcagCCTCTTGTATCAGGTGCTGCACTGGGATTGGAAGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - - - - - - ggaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa