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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG

Basic information

species Glycine max
transcript GLYMA15G07330.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                                   ||||  |   ||| | | | | |||  | ||| |  | ||  | |     ||  |||   |    || |  || | ||||||||||| ||||| |||||||| || ||||||||    || |||||||||||||||||||||||  | |||||||| | ||||||||| ||| |   ||
--------------------------------gtaagttctacaattgttgttaataggt--tgtaattaatgtagtt-taattgatgatcaaatacct-cttttttcttttagATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                              | |||| | |    |   |||   | |  |  | |   ||||||   |      | || | ||  ||    | | ||     |||| ||||| ||||| ||||| || || ||||||||| |||| || || |||||||||||||||||  | |||||||||   ||  |||| ||| | || |
------------------------------gtaagattatt---tcctattcagcatttt--tcttctttttttcttttgtttgagttctaacatata---tgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgt----agATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                |  | || | ||         |      | | | ||   ||    || |   || |||||  | | |||||||    || ||   | | || || |    |||||||||| |||  ||||||||| || ||||||||   ||| ||||||||||| ||||| |||||| | ||||| |||| |||| |||| ||  |    |
--------------gtaagtcttattat---------tcctctttgtaacttatattaagaattttgtttctttaa--aactaaaattt----ggttttcttcttctgatattttcagATTCTTGGCAGTAACATGTCAAATAAGATGTGGGAAAGTCTTGTTGAGCATGCGAAGACATGTGTTTTGAGTGGCAAACACTATATATATTACTCAAGCG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggatta-actatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                     |||  ||| |   | |||   |  ||  | | | |   |  | | |  ||||||  | |   |  || | ||   | |  || | ||    ||||| ||||| ||||| ||||| ||||||||||||||||  || || || |||||||||||||||||  | ||||| |||   ||  |||||||| | ||||
----------------gtaagttcgtatgtgggtgtgttattaacttactattatt--atactttca--tttttatgtgtttcagtttatgactattaatgctcttctgtgatagATACTTGGAAGTGGTATGTCCAACAAAATGTGGGATGCCCTTGTGGAACATGCAAAGACTTGTGTCTTAAGTGGGAAATATTACATATACTATTCTGATG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttg--gtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                             | ||    | | |    || |||  |||    |  | | | || |   | |  | | |   ||             || |  | |||||||| || ||||| |||||||| || ||||||||    || ||||||||||||||||| |||||  | |||||||| |  |||||||||||| |    |
-----------------------------gtaagttctatgatacctgtttttgcttactatattgtgatttatggtattccctatatggtttgacagcccttgttctttttatagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGAGCATGCAAAGACATGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                                   ||||  |    ||||      | ||||| ||   | |||  ||||   |   ||| ||        |    |  |||||||||| || ||||| |||||||| || ||||||||    || ||||| ||||||||||| |||||  | |||||||| |  |||||||||||| |    |
--------------------------------gtaagttcta----tgataccttattgtgatttatggtatttc-ctatatga---tttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G018837_T01 (Zea mays), 3'ss of exon 6
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcac-ggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                           |  |   | || |  ||| | |||  ||||  |  ||  |   ||| |  | |      |  | |    |    |||| ||    ||||| ||||| ||||| ||||| ||||||||||||||    || || ||||||||||||||||||    | |||||||||   ||  |||||||| | ||||
--------------------------gtaagtttgtgtgtgcagtgttatt-aacttattcttactatactttcatgtgttttggttgctgattataaatgctattctgtgatagATACTTGGAAGTGGTATGTCCAACAAAATGTGGGAAACCCTTGTGGAGCATGCAAAGACTTGTACCTTAAGTGGAAAATATTACATATACTATTCTGATG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatc--ctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                              | |||| | |  | |||| | | | ||    || | |||   |  | | |    |||||| |   |||      |   |  ||||||||||||| |||||||||||||| || |||||||||||||| || ||||||||||| ||||||||||| ||||| ||||| ||||| |||||||| ||||
------------------------------gtaagaatgtacattttgttgtcatttcagaatttgaatccgtctattgt----aatttttatttatttgtctccaattgttgtagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATGTTCTTGTGGAGCATGCAAAAACTTGTGTTCTAAGTGGGAAACTTTATGTTTACTATCCTGATG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttca-cggat-taactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                                                   | | |     |  | | ||||||   | ||      | ||| |  || ||  |   ||   | |||||||||| |||||||||||||| || |||||||| |    ||| |||||||| || || || || || || ||||| || ||||| || ||| |||| |
--------------------------------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

upper sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                                   |||    |||||  ||     |  |  | |   ||| ||       ||      ||| |   ||  |   ||   | |||||||||| |||||||||||||| || |||||||| |    ||| |||||||| || || || || || || ||||| || ||||| || ||| |||| |
--------------------------------gtaagtaatgagtttttttctctctctttctctctctttctt------tcag----ctcatg---tagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

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|4260437|gb|AI416933.1|AI416933
EST:     TTGAAGATGTCGTACAACTTGTGGTCAGAGATCCACAGAGATTGCGGAAT                         ATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCAT
genomic: TTGAAGATGTCGTACAACTTGTGGTCAGAGATCCACAGAGATTGCGGAATgtaagaatct ... cctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
                                   gattaac  putative branch site (score: 2)
                                         ctatcctc  CT-rich tract
     taaattttttaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA