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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacctttgtagacaaaattggttgtttttcatggtgatcatgtaattgctcaaagagtccttttcgtggtaattacattgcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA

Basic information

species Glycine max
transcript GLYMA02G17410.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
tacctttgtagacaaaattggttgtttttcatggtgatcat-----gtaattgctcaaagagtccttttcgtggta-attacattgcttga--tgtatttttgt-gcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
       |||   |||| | |||||   | |||    | ||     | | ||| |  |    |  |  | |   || ||||  |||||     ||||| |||||   |||| |||||||||||||| || || ||||| || |||||||| ||  | ||||||||||| || ||||||||||| |||||||| |||| ||   |||| |
------agtacg-aaaactagttgtaaattatgcaatttataaccagcagttgtt--atccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 22
--------tacctttgtagacaaaattggttgtttttcatggtgatcatgtaattgctcaaagagtccttttcgtggtaattacattgcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
        ||| |||| || | || | || | |      | |||  || ||  ||| |    ||||   |    || | |  |||  |  || || | |||  || |||||||||||||||| || ||||| || |  || ||||| |||||  | ||||||||||| |||||||||||||| || ||||| |||| || | | || |
tcaatgtctacatttg-aggcgaattgggatatgaaattttgtg--ca-gtgtttgtttt--gagttggtaaattgctcac-acacagtgtggtg-actttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGGTCAAGGAAAAAGACAACGCTAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 27
tacctttgtagacaaaattggttgtttttcatggtgatcatgtaattgctcaaagagtcct-tttcgtggtaattacatt---gcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
                               |    ||  |    |  ||   |   |  | | | ||  |   | |        || |||   || |||  |||| ||||| ||| | ||||| || |||| |||||||||||||||  | |||||||| |||||||| |||||||| || || ||  | | || | |  |||
------------------------------gtaaaaatgctacggtcacttgcattattttgtcttgtaatctctgctcctgaatttaatggccttgtgtttagGTTTGTGCGAGTATATCATCGGATTCAAAAAATATGAATGAGCTCGTTCAATGGAACGACCTCTACGGAGAAGGCGGGTCGAGGCACAAGACACCGTTGA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 6
taccttt---gtagacaaaattggttgtttttcatggtgatcatgtaattgctcaaagagtccttttcgtggtaattacattgcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
 || |||   |   |    ||  |   ||||  |  ||| |  |  | |||| ||      |   |   | |     ||| |    | || | |||  || ||||||||||||||||  | || || || |  || ||||  |||||  | ||||||||||| |||||||||||||| |||||||| |||| || | | || |
-acatttgaggcgaatgggatatggaattttgtacagtgtttgta-atttgcccatttgagctggtaaattgctcacacaatatggggtg-actttcttgtagGTGTGTGCAAGTGTTCCCTCGGATTCCAGTAACATGAGCGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGATCAAGGAAAAAGACAACGCTAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 26
-----tacctttgtagacaaaattggttgtttttcatggtgatcatgtaattgctcaaagagtccttttcgtggtaattacattgcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
      |    ||| |        |     ||||||   | ||  | |   |  | |||  |||||    |  | | | || |   |  |||  | ||  ||||||| |||||||| || || ||||| || ||||||||||  |||||||| |||||||| ||  | ||||||||||| |||||||| || | |  ||| || |
agaagcaaacatgttgttttggccgacatattttca--ataatattttctgtatttaaa--gtcctgcaagaagca-taacttcattccatgattcttgatgcagGTATGTGCAAGCGTCTCTTCAGAATCTACAAATATGACCGAGCTACTGCAATGGAACGAATTATATGGAGAAGGTGGATCAAGGAAGAGGGCATCCCTCA

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|19269058|gb|BM885314.1|BM885314
EST:     GTGACATTCGTCCCTTAAAGATGGATGATTTTAGATATGCACATGAGCAG                         GTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAA
genomic: GTGACATTCGTCCCTTAAAGATGGATGATTTTAGATATGCACATGAGCAGgtatatcaat ... ttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctcaaagagtccttttcgtggtaattacattgcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
                                  gcttgat  putative branch site (score: 5)
                                          tattttt  CT-rich tract
                        taattacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctttgtagacaaaattggttgtttttcatggtgatcatgtaattgctcaaagagtccttttcgtggtaattacattgcttgatgtatttttgtgcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
-acctttg
- - - - -agacaaaa
- - - - - - - - - -ggttgtt
- - - - - - - - - - - - - - -catggtg
- - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga