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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattctaattttctctgtggcctctctttcctcaactcaattggggtttatctgttaactcacaatcggctttacttttca

Basic information

species Glycine max
transcript GLYMA17G37820.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 14
CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtac--attctaatt--------------ttctctgtggcctctc-tttcctcaactcaattggggtttatctgttaactcacaatcggctttacttttca-----
  |||||||| || |||||||||||||||||||| || ||| |||| || |||||||| || |||||||| ||||| || |  || |   || ||   |||||||  |  || |||               || ||      | || |||| |    || |     ||  |      |||| |   |    |  | | || |     
-CAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTACTCGAGATCAACCCCAGGCACCCCATCATCAAGGAACTCCGTGACAAGGTCGCCCAGGACAGCGAGgtactgaagcttattagatcgacaaaaacctcactaatatttatcatttctttgcttccaaatacgtcgaaaaaaaaacttatggttttgtgcaatcttgatgcag

upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 14
CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtac------attctaattttctctgtggcctctctttcctcaactca-----attggggtttatctgttaactcacaatcggctttacttttca---------------------------------------
  |||||||| || |||||||||||||||||||| || ||| |||| || |||||||| || |||||||||||||| || |  || |   || ||   |||||||      |   ||  |  ||||     | ||   || | ||  ||       | |  |  ||  ||      |  |   |    ||  | |                                        
-GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTGGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtacctaattaccttagctagctctagctgcacttgctcgttaaaccatgggagctagcatgcatgcgtgggaggatgaaatgaaacacgatgctgattcgtttgttcgttggttcgtaaaacaacaacaacag

upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacatt--ctaattttctctgtggcct-ctctt------tcctcaactcaattggggtttatctgttaactcacaatcggctttacttttca-----------------------
  |||||||| || |||||||||||||||||||| || ||| |||| || |||||||| || |||||||||||||| || |  || |   || ||   ||||||| ||  || |  | | || ||   | ||| |        | ||    ||   |  |   |  |   |     | |||  | | | | |                         
-GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag

upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 14
CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattctaat--tttctctgtggcct-ctctttcctcaactcaattggggtttatctgttaactcacaatcggctttacttttca-------------
  |||||||||||||| ||||| ||||||||||| |||||| | || || ||||| || || ||||||||||| |  || |||||||||||| ||  |||||||  || ||     || | |||    | ||   |  || |  || ||    |      ||||  |   |    |    ||||   |             
-CAGCAAGCAAGCATATATGCGTGGCAAGAGGGTGCTTGAGATAAACCCAAGGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgttttagagacttttttgtcatttacttaattgtctatgcatttcttataacctggttatgtaggagcatggcacacttaaaatgtatctttatga

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|58024657|gb|CX711398.1|CX711398
EST:     AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGA                         GGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
genomic: AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattct ... ttacttttcaGGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
EST: gi|48575291|gb|CO036330.1|CO036330
EST:     AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGA                         GGATGAGGGTGTGAAACATACAGCACAGTTGATGTAC
genomic: AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattct ... ttacttttcaGGATGAGGGTGTGAAACATACAGCACAGTTGATGTAC
EST: gi|193630748|gb|FK580927.1|FK580927
EST:     AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGA                         GGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
genomic: AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattct ... ttacttttcaGGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
EST: gi|298171035|gb|HO016067.1|HO016067
EST:     AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGA                         GGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
genomic: AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattct ... ttacttttcaGGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
EST: gi|192324322|gb|FK018298.1|FK018298
EST:     AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGA                         GGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
genomic: AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattct ... ttacttttcaGGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
EST: gi|5687855|gb|AI940834.1|AI940834
EST:     AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGA                         GGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT
genomic: AGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattct ... ttacttttcaGGATGAGGGTGTGAAACATACAGCACAGTTGATGTACCAGACCGCACTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacattctaattttctctgtggcctctctttcctcaactcaattggggtttatctgttaactcacaatcggctttacttttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC