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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatcgttcatgtctgggtggtcttatatgtgtatattcttgtttgctaatattatttccctgttatgtttatgtttaaatctctgcaatag

Basic information

species Glycine max
transcript GLYMA10G41920.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41920.2 (Glycine max), 5'ss of exon 21
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 5'ss of exon 21
GGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatcgttcatgtctgggtggtcttatatgtgtatattcttgtttgctaatattatttccctgttatgtttatgtttaa-atctctgcaatag
|| ||||| || ||||||||| || |||| |||||| | |||||| | |  |||||||||||||||||||| |  |||||||| |  ||||||||| | |    || ||    |    || |  |  ||| ||| |   |   || |||||||    ||| |  | |  |||   ||   ||||  ||
GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACAGTGGAAGTCAGATTGTTTGACAAACTGTTCCTCTCTGAGgttggcaaacaggaatctc---ataaatttct--gcttatgttcct-cctaagaaaattatttttgggttcttatgagatttcctattattgcatcag
















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|17401220|gb|BM178002.1|BM178002
EST:     ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATCAGAG                         AATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
genomic: ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatc ... tctgcaatagAATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
EST: gi|20812918|gb|BQ297396.1|BQ297396
EST:     ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTATTCCTATCAGAG                         AATCCCGCTGAACTTGACAACTGGCTTGGCGATTTGAACCCAAATTCCAAA
genomic: ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatc ... tctgcaatagAATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
EST: gi|58022687|gb|CX709428.1|CX709428
EST:     ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAG                         AATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
genomic: ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatc ... tctgcaatagAATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
EST: gi|19346023|gb|BM890903.1|BM890903
EST:     ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAG                         A-TCCCGCTGAACTTG
genomic: ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatc ... tctgcaatagAATCCCGCTGAACTTG
EST: gi|298189813|gb|HO038216.1|HO038216
EST:     ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATCAGAG                         AATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
genomic: ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatc ... tctgcaatagAATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
EST: gi|17401215|gb|BM177997.1|BM177997
EST:     ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATCAGAG                         AATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA
genomic: ATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatc ... tctgcaatagAATCCCGCTGAACTTGACAACTGGCTTGGCGATTTAAACCCAAATTCCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAGgttggctatcgttcatgtctgggtggtcttatatgtgtatattcttgtttgctaatattatttccctgttatgtttatgtttaaatctctgcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT