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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttacatttgacattggtgtgtaaaaatttgctgaaatttggagtctttgaggaagaaattttttaatcatttttttctggcacttcacatatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGTTACCTTTGCAGAGATTTCTGCACTTCGATTTTTATGTACTCAG

Basic information

species Glycine max
transcript GLYMA10G35210.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35210.2 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os04g14654.1 (Oryza sativa), 3'ss of exon 21
ggtttacatttgacattggtgtgtaaaaatttgctgaaatttggagt-ctttgaggaagaaattttttaatcatttttttctggcacttcacatatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGTTACCTTTGCAGAGATTTCTGCACTTCGATTTTTATGTACTCAG
|| ||||| |||| || || | | | ||||| | | ||| | | | | || | |||| | ||| | | || | | | | | |||| ||| || |||| | ||||||||| |||| || ||||| |||||||||||| |||| |||||||| | || |||||
---ttgcattt-acat-ggaaaatactgttcttgtcaaattcctaatacttcgtagcatgtttcttctcttcatctgtttttatt--ctaacgtgtgtttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTTTGCAGAGATTGCTGCTCTTCGATTCCTTAGTTCTCAG
















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|192303192|gb|FG997768.1|FG997768
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|192334522|gb|FK024481.1|FK024481
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|207807592|gb|GD776611.1|GD776611
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGGTTGGGGGCG
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTG-TTGGGGGCG
EST: gi|192334521|gb|FK024480.1|FK024480
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|192301842|gb|FG997700.1|FG997700
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|213605266|gb|DB978740.1|DB978740
EST:     AGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTCGTCTTTGTTGGGGGCGT
genomic: AGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|120493752|gb|EH221919.1|EH221919
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|120493838|gb|EH222005.1|EH222005
EST:     TATCA-GGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: TATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|208086974|gb|GD883340.1|GD883340
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|208275482|gb|GE078186.1|GE078186
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
EST: gi|192303193|gb|FG997769.1|FG997769
EST:     AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAA                         AGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT
genomic: AATAGCCCATCATTTGACACTTTATCAGGGATTCAATCCAGCATAGCCAAgtatgtttac ... catatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttgaggaagaaattttttaatcatttttttctggcacttcacatatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGTTACCTTTGCAGAGATTTCTGCACTTCGATTTTTATGTACTCAG
                  ttttaat  putative branch site (score: 3)
 aagaaattttttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttacatttgacattggtgtgtaaaaatttgctgaaatttggagtctttgaggaagaaattttttaatcatttttttctggcacttcacatatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGTTACCTTTGCAGAGATTTCTGCACTTCGATTTTTATGTACTCAG

- - - - - - - - tggtgtg
- - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - -gtctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttca