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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatggtgtaataattatgagtttcatctgttggaatccctatttttttatgggctaaggtttaccagaactcgtgtatcagtctagaatacttgtcttgttgtgtttgctttgtcataccttttcataatgtaagaggcgtttcttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCA

Basic information

species Glycine max
transcript GLYMA17G37820.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 11
ggtatggtgtaataattatgagtttcatctgttggaatccctatttttttatgggctaaggtttaccagaactcgtgtatcagtctagaatacttgtcttgttgtgtttgctttgtcataccttttcataatgtaagaggcgtttcttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCA-
| | ||| | | || | || || | | ||||| ||| |||| | | | || ||| | || |||| || | | || | | |||||||| || || || |||||||||||||||||||||| ||||| || || || ||||||||||| || || |
--------------------------------------------------------------------------------------------------------------gtaagattgggttttccgcagtg---aatgcaagtcacatactctgta-attatctttaaagtactgaaaagatttttctctaat---cagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 13
ggtatggtgtaataattatgagtttcatctgttggaatccctatttttttatgggctaaggtttaccagaactcgtgtatcagtctagaatacttgtcttgttgtgtttgctttgtcataccttttcataatgtaagaggcgtttcttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCA-
| |||| | || | | ||| | | || || | ||| | ||| | || | | | | | || || | || | |||| || | | ||| | | |||||||| || || || |||||||||||||||||||||| ||||| || || || |||||||| || || || |
-------------------------------------------------------------------------------------------------------------gtaatgtctttccccccc-tgctgtga-atgcaagtcacatgctctatat-ttgtcattacaatgctaaaagtaggaacaactg-taatcagATGAAGAGAAAAATGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATTGAAGACGCAAC

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 11
ggtatggtgtaataattatgagtttcatctgttggaatccctatttttttatgggctaaggtttaccagaactcgtgtatcagtctagaatacttgtcttgttgtgtttgctttgtcataccttttcataatgtaagaggcgtttcttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcaca-
||||||||| | | | | | || | | | ||| | | || | | | |||||| | | | | ||| | | | || | ||| || || | ||| | || ||| ||| | |||| | | | | | ||||| |||| | | || | ||| ||| || |||||||||||||||| ||| | |||||||||||||||||||| || ||||| ||||||||||| || || |||||
-gtatggtgtcgttaatgtcacaatcttgttctaacttccagaaaatatttt---------tctcccagaa---gcaatttgcttttaaattttaattgattgctgcctatcttgcaatggattctagtaac---tgttgctgctctctcatttctcttgccatctttat--tgatgttgagttccaatat-attgcagATGTTGAAAAGTCCAGTGATGATGATGAGAAGAAAGGTCAGTATGCAAAGTTCTGGAATGAGTTTGGCAAGTCCATAAAACTTGGTATTATTGAAGATGC--

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|193352039|gb|FK315494.1|FK315494
EST:     GTAGGATTGCTGATGAGGATCCTGATGAGTCCACTGACAAAGAAAAGAAA                         GAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTC
genomic: GTAGGATTGCTGATGAGGATCCTGATGAGTCCACTGACAAAGAAAAGAAAggtatggtgt ... ttgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTC
EST: gi|10848102|gb|BF071680.1|BF071680
EST:     GTAGGATTGCTGATGAGGATCCTGATGAGTCCACTGACAAAGAAAAGAAA                         GAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTC
genomic: GTAGGATTGCTGATGAGGATCCTGATGAGTCCACTGACAAAGAAAAGAAAggtatggtgt ... ttgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTC
EST: gi|193590608|gb|FK544499.1|FK544499
EST:     GATGAGGAT-CTGGATGAGTCCACTGACAAAGAAAAGAAA                         GAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTC
genomic: GATGAGGATCCT-GATGAGTCCACTGACAAAGAAAAGAAAggtatggtgt ... ttgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCA
                                           tattgat  putative branch site (score: 3)
 atcaatattaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatggtgtaataattatgagtttcatctgttggaatccctatttttttatgggctaaggtttaccagaactcgtgtatcagtctagaatacttgtcttgttgtgtttgctttgtcataccttttcataatgtaagaggcgtttcttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG