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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggaaatttgctcttaattggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA

Basic information

species Glycine max
transcript GLYMA14G06340.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
--------------------------gtgtggaaatttgctctta--attggaactattttttggtttcagctgtggaaatctcagattat----tgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
                          |||   |    ||||  |    ||| ||   |    ||  |   | |   |   | | |  | ||    |||    | |      |||| |||| ||||||||  | || ||||||||  |  ||||||| || |||||||||||||| || ||||||||||| || |||||| | |||||||| ||||
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatttctggagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
----------------------gtgtggaaatttgctctta-attggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
                      |||   |   ||| | ||  | |||    ||  ||   ||    ||||    |  | |  |   |||  | | |   |  |||| | || ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || ||||||||||| || |||||| | |||||||| ||||
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgctt--attgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 6
-------gtgtggaaatttgctcttaattggaactattttt-tggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
             ||| | ||     | | |  | |||  | | | | | ||| |   ||| | | |  || ||  | | |   |  |||| |||| ||||||||  | || ||||||||  |  | || || || |||||||||||||| || |||||||||||||| |||||| | || ||||| || |
gtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgctttt--aatttaataacat-gtgttaatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
-------gtgtggaaatttgctcttaattggaactattttt-tggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
             ||| | ||     | | |  | |||  | | | | | ||| |   ||| | | |  || ||  | | |   |  |||| |||| ||||||||  | || ||||||||  |  | || || || |||||||||||||| || |||||||||||||| |||||| | || ||||| || |
gtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgctttt--aatttaataacat-gtgttaatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 25
-------gtgtggaaatttgctcttaattggaactattttt-tggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
             ||| | ||     | | |  | |||  | | | | | ||| |   ||| | | |  || ||  | | |   |  |||| |||| ||||||||  | || ||||||||  |  | || || || |||||||||||||| || |||||||||||||| |||||| | || ||||| || |
gtaaaataaaaataaaatagccagacagtcgtgcaattcctgtcgctaccgctttt--aatttaatagcat-gtgttaatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
gtgtggaaatttg---ctcttaattggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacg---cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
  ||   | |||    || |  || |     |  |||   ||||  ||    ||||   |  |||| |||||       | ||    ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || ||||| |||||||| || ||||||||||||||||| ||||
--gtaagagtttaaatctatctatcgagtacacatttatatttcccctt---aaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 26
---gtgtggaaatttgctcttaattggaactattttttggtttcagctgtggaaa----------tctcagattat-tgttattactgtatacg-------cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
     ||  |||| | ||     ||  |  |||||| |   || |    ||||||          |   |||| || |  | || ||||  | |       ||||| || || || || ||| |||| ||||||||||| ||||||||||| |||||||| || || || |||||||| || ||||| || |||||||| || |
gtaaagttcaaatatactacccctttaa--tattttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtgaatggtgcgaacagATCGAGAAACACGAACTTGTTGAAATGAGACGTGTGGCTGCTTATATCTACAAGAAAGCGGGCAGATGGAAGCAATCAATTGCATTATCAAAGAAAGACA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
gtgtggaaatttgctcttaattggaactattttt-----tggtttca-gctgtgga-aatctca-gattattgttattac-tgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
|||  | |   |    |||  || || | |||||     |||||  | ||  |||   || |||  |   |||||  ||  ||| |  ||||||||| || || |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| || |
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA

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|151406151|gb|EV275966.1|EV275966
EST:     ATTTGCACGATAACTTTGATCAAATAGGCCTTGCTCAAAAG                         ATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: ATTTGCACGATAACTTTGATCAAATAGGCCTTGCTCAAAAGgtgtggaaat ... gtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
EST: gi|6481487|gb|AW200758.1|AW200758
EST:     AGTCAATTGATTTGCACGATAACTNTGATCAAATAGGCCTTGCTCANAAG                         ATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: AGTCAATTGATTTGCACGATAACTTTGATCAAATAGGCCTTGCTCAAAAGgtgtggaaat ... gtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA
                            agattattgttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggaaatttgctcttaattggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG