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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgcttttaagtatgtttgattctgctatttagaattcacatctgtgcaagaattaataatgaatttctgttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG

Basic information

species Glycine max
transcript GLYMA02G01220.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 8
----------gtatcttgcttttaagtatgtttgattctgctatttagaattcacatctgtgcaagaattaataatgaatttctgttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
            ||  |     | ||  | || ||   | |   | |         ||||   |||  |||    |   ||| |||| ||   |||||||||||||||| || ||||| || ||||||||||||||||| ||||||
gtaagagatcacattatttacatgaggcttttggaccatccagctcattgcaactgtctgcctaagctttatcctt---tttttgtt-ttaaaagCCTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAG

upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 8
gtatcttgcttttaagtatgtttgattctgctatttagaattcacatctgtgcaagaattaataatgaatttctgttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
|||  |      |   | |   ||  ||  |  |  |  |  |     | ||   |  |  |   ||| | |   || ||   ||||||| |||||||| || || || || ||||||||||||||||| ||||||
gtaagtgatcactccatgtacgtgggtcatcagtggactaccccagcttatgtctgcctacaatctgattgttcttttttaacagCCTCTGTTCCCTGGAGAAAGCGGTGTTGATCAGCTTGTTGAAATCATCAAG
















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|193403349|gb|FK367699.1|FK367699
EST:     TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCGGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|207824407|gb|GD793767.1|GD793767
EST:     TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|193398127|gb|FK361249.1|FK361249
EST:     GATATCTGGTTCTAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCGGCTTGTTGAAATTATCAAG
genomic: GATATCTGG-TC-AGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|15286220|gb|BI470111.1|BI470111
EST:     TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|10254836|gb|BE822602.1|BE822602
EST:     TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|298195934|gb|HO044325.1|HO044325
EST:     TTGATGTCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|9259545|gb|BE347700.1|BE347700
EST:     TTTTTATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAT                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|37994511|gb|CF806247.1|CF806247
EST:     TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
EST: gi|27425418|gb|CA936938.1|CA936938
EST:     TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAG                         CCTCTATTCCCT
genomic: TTGATATCTGGTCAGCCGGTTGTGTACTTGGTGAACTATTGCTTGGCCAGgtatcttgct ... ttgttgttagCCTCTATTCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttagaattcacatctgtgcaagaattaataatgaatttctgttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG
                          aattaat  putative branch site (score: 3)
                                       tttctgtt  putative PPT
                       aagaattaataatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttgcttttaagtatgtttgattctgctatttagaattcacatctgtgcaagaattaataatgaatttctgttgttgttagCCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT