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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaataatatttgtatcggatttacattaatgcaatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC

Basic information

species Glycine max
transcript GLYMA17G12850.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaataatatttgtatcggatttacattaatgcaatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC
  |   || | || | |    |  | | |  |    |    |  |     || |||        || |    |   || | |  |   ||   ||| ||||| |||||||| |||||||| || || || || ||||| ||||||||||||||||| || || || ||  |  |||| |||||| | ||||||||
acttggatcagcaaatattctgtctgtagtagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgtgagttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC

upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaa-agaataatattt---gtatcggatttacattaatg-caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC
   ||  ||| |||   | |    ||  |   | |    |  |  | |  ||||  || | | | | |||    |||  | | | | || | || |   |  ||||| |||||||| || ||||| || ||||| || ||||| |||||||||||||| || || || || ||| | ||||| |||||| | ||||||||
--ccttttaatcatgtgattg---tacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC

upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 19
-----------------------------------------------------------------------------cttctcataaccatacaaataggatattggggt---agggtg--taaagaaatgacatgttaaagaataatatttgtatcggatttacattaatgcaatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC
                                                                             || |     | | | ||| | || | ||||  |   ||| ||  |    |  | |  |  || |    || | ||   | | | | | ||| |  || ||  ||||| || ||  |||| ||||||||||||||||| ||||| |||||||| || || || ||||||||||||||| |||| |||||| | || |||||
gtaccttgttgaactcattaaatattgcaaggcctgaaatttataatagataagaaaaacacagaagttctcaatttctgcaagagaactttcaagttgg-tgttggcatgccaggatggttttgaatgtaaagtactacatgtcaagaatttgtttgtactgaaattga--catttggcagGGGACCAGCCGACCCGCTCATTATCATGTTCTCTGGGATGAGAACAACTTTACAGCAGATGAGATCCAATCTTTGACGAACAACCTCTGTTACAC

upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 18
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaataatatttgtatcggatttacattaatgcaat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC-----
                                      ||||    ||| ||   |         |  | |  | |    |||    |  | || |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| ||||   | || || || ||||||| | ||||||||||     
--------------------------------------gtaacatgatggcaccct----ggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG

upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaa-taatatttgta---tcggatttacattaatgcaat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC-----
                                               | || || |  ||   |    ||||||   | |    |||    |  | || |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| ||||   | || || || ||||||| | ||||||||||     
----------------------------------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG

upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 18
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaataatatttgtatcggatttacattaatgcaat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC-----
                                      ||||    |||      |         |  | |  | |    |||    |    || |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| ||||   | || || || ||||||| | ||||||||||     
--------------------------------------gtaagttgatggagccct----ggcctttgtagctttgctcatacgacgagattatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG

upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 18
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaa-taatatttgta---tcggatttacattaatgcaat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC-----
                                               | || || |  ||   |    ||||||   | |    |||    |  | || |||||||| ||||| |||||||| || ||||| || || |||||||||||||| |||||||| ||||   | || || || ||||||| | ||||||||||     
----------------------------------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCACACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG

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|31466814|gb|CD408842.1|CD408842
EST:     CAGTCATGCGGGAATTCAG                         GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
genomic: CAGTCATGCGGGAATTCAGgtatgataat ... caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
EST: gi|207835146|gb|GD806823.1|GD806823
EST:     GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAG                         GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
genomic: GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAGgtatgataat ... caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
EST: gi|193674915|gb|FK616033.1|FK616033
EST:     GTCATCCTACGGAATTCGACTTCTATTTATGTAGTCATGCAGGAATTCAG                         GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
genomic: GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAGgtatgataat ... caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
EST: gi|26269215|gb|CA820278.1|CA820278
EST:     GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAG                         GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
genomic: GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAGgtatgataat ... caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
EST: gi|15285585|gb|BI469476.1|BI469476
EST:     GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAG                         GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC
genomic: GTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAGgtatgataat ... caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgacatgttaaagaataatatttgtatcggatttacattaatgcaatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC
                                     cattaat  putative branch site (score: 3)
      atgttaaagaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaataatatttgtatcggatttacattaatgcaatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - ccataca
- - - - - - - - - - - - - - -gggtagg
- - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaataa