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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA

Basic information

species Glycine max
transcript GLYMA15G18470.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
ctgaactaattattgtttcaaaactattgtaattctttgt-tgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
      ||| | ||| |   ||| |||| |  | ||   | |  ||   ||  || | | || | | |             | |||   ||  || || || ||||| || || || || ||||||||||| |||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||| | || ||||| |||
-----gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaa-------------agattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
ctgaactaattattgtttcaaaactattg-taattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
 |   |||| | |    | |  |   ||  |  ||| | |||| || | ||  ||   |||  |  || | | ||    ||| ||||          | || ||| | || || || |||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| || ||||||||| | || || || |||
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactca-tattacaaaattctggtca-attt-------ctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
        |   |   |   || ||| | |  ||   | ||  |  |  |||    | || |  |  ||| ||     |  |||    ||   |  | || || || || || || |||||||||||||| |||||||| || ||||| ||||||||||| || || || || |||||||||||  | || || |  |||
------gtacgctgaatctgaacctactatctttacatttttatagatgatt-caacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttca--tatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
    | |  |  ||  || || | | ||      | |  |||| |   | || |        | || | | | ||||   |  ||||       |   |||| |||||||| |||||||||||||||||||| ||||||||||||||||| |||||||| || ||||| || ||||| ||||||||  | || |||||||||
--atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttttttttaattttatgtctctgttctcctaattattattttttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
----ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
    ||    |  |  ||  ||| |   | | |  ||  || | ||     |||   |    | | ||||   |  |    ||  |  ||||       | ||| ||||||||||| || || |||||||| || ||||| ||||||||||| |||||||||||||| || || || || || |||||  |  ||||| | |||
ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgt-tgttacttgat---tcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
-----ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
      |  | |        | | | |||||    | ||  |     | | |  | |  ||| |   |  | |  | |  | |   |  ||||   |   | ||| || || ||||| ||||| |||||||| |||||||||||||| |||||||| |||||||||||||| || || || ||||||||  |  | ||| | |||
ttcttttacattggaccacatct-agaactaccaca-ttaatcagaatgtcaggacttagccttggtt--tctgcactgacctat-tggttgattcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S43_35V6.1 (Physcomitrella patens), 3'ss of exon 2
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccc---tccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
      | |   |    ||  ||   ||   ||   || |      |||  || |      ||     |||  | || |  |  || ||||       | ||| ||||||||||| ||||| || ||||| || ||| | ||||||||||| |||||||| |||||||| || || || || |||||  |  ||||| |||||
---ctttcaccttcacatctgaatatttaggatgtattttgaccagactggtaaggttgtgtcttgattattgacttacggtagtagttgatttcaactgcagGTATGTGGCCCCGGAGTACGCTATGACAGGGCATTTACTTGTGAAGAGTGATGTTTATAGTTATGGAGTGGTGCTTCTGGAGCTCCTTTCTGGACGAAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S255_47V6.1 (Physcomitrella patens), 3'ss of exon 6
-------ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
        || ||     |||   || |||  || |  ||  ||     | |||  ||  |||| |   |  |  |    |      ||||| ||   |   | ||| |||||||| || || || |||||||| |||||| | ||||||||||| || ||||| |||||||| || || || || |||||  |  | ||  | |||
tgtttctttgcaccgg--attacctccaaa--atggccatatttgtcactattaggatcgtgccttggtttctgcac---tgacaaaatattggatctaaactgcagATATGTGGCTCCTGAATACGCAATGACAGGACATTTGCTTGTGAAGAGTGACGTTTATAGTTATGGAGTGGTACTGCTCGAGCTCCTCTCGGGGCGTAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ34792 (Selaginella moellendorffii), 3'ss of exon 2
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
                                         ||     |  |    | |   |  | ||||| || | |||| | |      || | |||||||||||| || ||||| || ||||| || || |||||||| |||||||| |||||||| || || || || ||||| ||| |  |  | || ||||||
-----------------------------------------gtacgttttctccatctttttt--tttatatcttatctcatgtgttcttttctctccagTTATGTGGCACCCGAGTACGCCATGACCGGTCACCTTCTTGTTAAGAGCGACGTTTACAGCTACGGCGTGGTACTCCTCGAGTTGCTCTCGGGTAGAAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ20296 (Selaginella moellendorffii), 3'ss of exon 2
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactatt-cagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
                            |||   ||||| | ||  ||      |   ||  | ||            | || | ||    |||    |||||| || || |||||||| |||||||| ||||||||| | |||||||||||||| ||||| || || ||||| || || |||||  || | || ||||| 
----------------------------gta-cgctttggttttcaacagcgtagttttcttttatcctctgagaaactgatctctggtttactggcgcagTTACGTCGCTCCAGAGTACGCAATGACCGGACATCTTTTGGTGAAGAGCGATGTCTACAGCTACGGGGTTGTGCTACTCGAGCTACTGTCGGGCAGAAAG

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ23539 (Selaginella moellendorffii), 3'ss of exon 4
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
                                             |||  || |  ||  | |  | | | | || | |||| | |      || | |||||||||||| || ||||| || ||||| || || |||||||| |||||||| |||||||| || || || || ||||| ||| |  |  | || ||||||
--------------------------------------------gtac-gttttctccatctttttttttgtcttatctcatgtgttcttttctctccagTTATGTGGCACCCGAGTACGCCATGACCGGTCACCTTCTTGTTAAGAGCGACGTTTACAGCTACGGCGTGGTACTCCTCGAGTTGCTCTCGGGTAGAAAA

upper sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ23292 (Selaginella moellendorffii), 3'ss of exon 2
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
       |  | | ||||  ||   |  ||| || | | ||||  |   |  |     || ||| |      |||||  |                 |||||| || || |||||||| |||||||| ||||||||| | |||||||||||||| ||||| || || ||||| || || |||||  || | || ||||| 
----gtaagctctggttttcaa--cagcgtagttttctcttgtcctctgagaaactgatctctggt------tttctggcg----------------cagTTACGTCGCTCCAGAGTACGCAATGACCGGACATCTTTTGGTGAAGAGCGATGTCTACAGCTACGGGGTTGTGCTACTCGAGCTACTGTCGGGCAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA
              ccctgat  putative branch site (score: 4)
                 tgatatatattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
ctgaact
- - - - - - - - - caaaact
- - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc