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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgctttttgcatcggttgagtttttaagggataattcttgtgaacctttttgtgttttggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAACTCTGTTGGTATGTGGTCTAAGCCCACGTTTAGGCGCAAAACGAAGATAG

Basic information

species Glycine max
transcript GLYMA09G23150.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------gttcgtgctttttgcatcggttgagtttttaagggataattcttgtgaaccttt-ttgtgttttggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAACTCTGTTGGTATGTGGTCTAAGCCCACGTTTAGGCGCAAAACGAAGATAG
||| ||| | || | || | | ||| ||| | || || | || |||||||| | || | |||||| || | || | ||||||||| ||||||||||||||||||||||| ||| |||| ||||| || ||||| |
ctggaatatttctatcagaagcagcgaacagctgcaaaggtaatcctcaatacaacttagtacttatcttaccggttttttgttgctctatgctgatcagGGAGAGGAGCAATATCATCTTTTACGGGGAATTCAACAGCTTGGTGAGACATCTGTTGGTATGTGGTCTAAGCCAACGGTTAGACGCAAGACAAAGATTG
















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|213595558|gb|DB972112.1|DB972112
EST:     AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAG                         ATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
genomic: AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAGgttcgtgctt ... tggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
EST: gi|209711150|gb|BW683804.1|BW683804
EST:     AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAG                         ATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
genomic: AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAGgttcgtgctt ... tggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
EST: gi|42723015|gb|CK768914.1|CK768914
EST:     AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAG                         ATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
genomic: AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAGgttcgtgctt ... tggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
EST: gi|7685590|gb|AW756238.1|AW756238
EST:     AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAG                         ATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
genomic: AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAGgttcgtgctt ... tggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
EST: gi|254335256|gb|GR846753.1|GR846753
EST:     AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAG                         ATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC
genomic: AATCAGCCCCTTCTGAAGTCATCCCCGTGTCACCCGAAGATGATCCAAAGgttcgtgctt ... tggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttgagtttttaagggataattcttgtgaacctttttgtgttttggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAACTCTGTTGGTATGTGGTCTAAGCCCACGTTTAGGCGCAAAACGAAGATAG
                                cctttttgtgtttt  CT-rich tract
 agtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtgctttttgcatcggttgagtttttaagggataattcttgtgaacctttttgtgttttggtgtttagATTGAGGAGCATTTGCAACATTTACGTGGGGTGCAGCCATTTGGTGAGAACTCTGTTGGTATGTGGTCTAAGCCCACGTTTAGGCGCAAAACGAAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA