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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA

Basic information

species Glycine max
transcript GLYMA17G37820.1
intron # 13
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 13
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
              |  |  |      ||||| ||| | ||||    | ||| || |  ||||  || |  || |  |||  |  | |     ||||   ||       | || ||||||        | |||||||| | |||||| || || ||||| || ||||||||||||||||| ||||| || || |||||||||||||| || || |||||||||||| | ||| 
-----------gggtactgcaccacatttatt-gcttttttatgagctcctccaatagaatta--ctctggatcc--ctggagcttaac----taatacttt-------tgttatcttttg------ttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
ggtgcaatttaaattgtttgatttttattatttgct-ctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
                         |||| | |||| ||  |  ||| | | ||   |  || ||  | |    ||||  ||     | |  |   | ||        ||  |  | ||||    ||  | ||||| || |||||||| || || || || || ||| ||||||| ||||||||||| || || |||||||||||||| || ||||||||||||||  ||||  
------------------------gtattttatgctgctggtggtttatccacttccattat-agtgtctgagatctg--gaatacagcttgtgggaagtaacgctgtcgcttgatttttttg--tttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 15
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgct-gaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
                    || | | |    ||||   ||||    ||   | | |   |  |   |   || | ||| |||  ||    |      |  |  |  |  |  |||  |||   |||  | ||||| || |||||||| || ||  | || || ||| ||||||| ||||||||||| || || |||| ||||||||| || ||||||||||||||  ||||  
------------------gtatatatgtatgctgctggtttatccactttcattacagtgtggggtctggaatacagcttgagaagtaccaacgctgcgcttgttttgttttgttttgttttgtttt--tgcagGTCATCTTCTTCACCGACCCTATGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAGGAAGTTCCAGAACGTGTCCAAGGAGGGCCTGAAGC

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
                                              |||  |     |||  |    ||||  | |           ||||| |        |  | |   || || |     | | |  ||||| || |||||||| || |||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| ||  ||||  
----------------------------------------------gtttgcattgcacacgaataattcttcttta---------aatgatctccaactcgcataacacgttctcatacttgtgttcc-cagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 13
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttt---tcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
 ||   |||  ||  | |        | || ||||| |   |   |   |  | |  |   | | |||  | || | || |||    ||  ||   | |   | |   || || | | |   ||| | |  | |||||||||||||| || || ||||| ||||| ||| ||||||||||||||||||| ||||||||||| || ||||| |||||||| ||||| ||  ||||| 
-gtatgattggaaaagata-------actacttgcttttcaaccgt---ccttgattagtctggtcttattcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATGGACTATGAAGACAAAAAATTCCAGAATGTGTCAAAGGAAGGCCTGAAAC

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 13
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttcta-ttctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
         ||||  | |  || |  ||| |||    || | ||| |  |      ||  | | | ||| |  || ||  |    || | ||  |     |   |||  | || |  ||     |||    ||||| || |  || || || ||||||||||| |||||||  ||| ||||||  || ||||| ||||| |||||||||||||  |||||||| | | | ||  
--------gtaaagcgctgtatctg-attgtttatagtagtttttggaacatgctcaagctcaacttttatggttttggcgcatagtca-gacatctcaacacttaa-tgaatatgattgcgggttt----cagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC

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|10848102|gb|BF071680.1|BF071680
EST:     CAACTGGAAAACTCTTCATTCCTTGAGCGGCTTAAGAAGAAAAATNTTGA                         GGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGAT
genomic: CAACTGGAAAACTCTCCATTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAggtgcaattt ... atttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGAT
EST: gi|4297522|gb|AI442630.1|AI442630
EST:     CAACTGGAAAACTCTCCATTCCTTGAGCGGCTTAAGAAGAAAAATTTTGA                         GGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGAT
genomic: CAACTGGAAAACTCTCCATTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAggtgcaattt ... atttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGAT
EST: gi|193523621|gb|FK478384.1|FK478384
EST:     CAACTGGAAAACTCTCCATTCCTTGGGCGGCTTAAGAAGAAAAATTTTGA                         GGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGAT
genomic: CAACTGGAAAACTCTCCATTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAggtgcaattt ... atttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA
             atttaat  putative branch site (score: 4)
                                  ttttcttttcaatttc  putative PPT
                                tattttcttttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG