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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacagttctgatttatgagtgagcaaggagttaacttcaactatatagcatgtactaggaaacagaactttattgatatacttgcagagtttaattatggtttcccttgctctaatactaatgaataccaaattgatttatgcacactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCATCAGCATTCATTTGATATTCAAACTGGAGAACAG

Basic information

species Glycine max
transcript GLYMA10G41110.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 9
gtaagcacagttctgatttatgagtgagcaaggagttaacttcaactatatagcatgtactaggaaacagaactttattgatatacttgcagagtttaatta--tggtttcccttgctctaatactaatgaataccaaattgatttatgca-cactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCATCAGCATTCATTTGATATTCAAACTGGAGAACAG
|| ||| | | | | | |||| | | | | | ||| || ||| ||| ||| | || | | | || ||| || | || ||| |||||||||| |||||||| |||| || |||||||||||||||||| ||||||| || ||||| ||||||||||||||||||||||||||
-----------------------------------------gtaaatatgttatactttgtttagatgagaaatctttataatttcttacattttttttttaaatggagacttttattttccttttattgataactcttatatttcatggggtgctttcagGGCATTTCAGGGGCTTTGCATTAATGAATTTAGTGGTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAG
















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|26056387|gb|CA799301.1|CA799301
EST:     AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATG                         GGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
genomic: AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATGgtaagcacag ... acactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
EST: gi|14259801|gb|BG882709.1|BG882709
EST:     AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATG                         GGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
genomic: AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATGgtaagcacag ... acactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
EST: gi|15285802|gb|BI469693.1|BI469693
EST:     AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATG                         GGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
genomic: AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATGgtaagcacag ... acactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
EST: gi|9899476|gb|BE608444.1|BE608444
EST:     AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATG                         GGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
genomic: AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATGgtaagcacag ... acactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
EST: gi|6070484|gb|AW099871.1|AW099871
EST:     AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATG                         GGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA
genomic: AATACCCCAATCATCTTCCGTTGGATTCCTAATGTTTCTCTGATTAGATGgtaagcacag ... acactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttcccttgctctaatactaatgaataccaaattgatttatgcacactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCATCAGCATTCATTTGATATTCAAACTGGAGAACAG
                                              cactttc  CT-rich tract
 taatactaatgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacagttctgatttatgagtgagcaaggagttaacttcaactatatagcatgtactaggaaacagaactttattgatatacttgcagagtttaattatggtttcccttgctctaatactaatgaataccaaattgatttatgcacactttcagGGCTTTTCAGGGACTTTCTATCAATGAATTTAGTGGTCTTCAATTTGACCATCAGCATTCATTTGATATTCAAACTGGAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA