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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG

Basic information

species Zea mays
transcript AC197122.3_FGT003
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 2
cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgatt-gtgatatatgt--tgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG-----
 ||  | ||||||| |      ||||    |||| || | ||||| ||| ||||  | ||||||||||| |||||   |||  | ||||||||  |||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||| || |||||||||||||| ||||| ||||     
-tttgtatgatatatt------ttgccgt-tgcaaatgacttttttgttaacattacttactgttctgggtttaacccatttataatatatgtgttgacataggttagTGCCTCTTATGAGCAGGCTCTTATGGATGCCCGAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTT

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g44900.1 (Oryza sativa), 3'ss of exon 2
cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgatt-gtgatatatgt--tgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG---------------------
                       |||    |||| || | ||||| ||| ||||  | ||||||||||| |||||   |||  | ||||||||  |||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||| || |||||||||||||| ||||| ||||                     
-----------------------tgccgt-tgcaaatgacttttttgttaacattacttactgttctgggtttaacccatttataatatatgtgttgacataggttagtgcctcttatgagcagGCTCTTATGGATGCCCGAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
cttcatg-tgatata-atactcgtttgcgaaatgca-gataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
 |   || || | |  ||| |  |||    | || | ||| || | | |   | | |  | |   ||| ||     | ||  |  ||  | || |||||| ||||||||||||| |||||||||||| || ||||||| || ||||  ||||| || || |||||| |||||||  |||||||||||||||| || || || |
ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataa--ctccttggcattgagtt-tgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 2
-----cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
      |   ||  ||  ||   || | | |  |||     |  |||||||  ||   |       ||   | |||||   |  || | | | ||  ||||||||||||||||||| ||||||||||||||| ||||||| || |||   ||||| || || |||||| |||| ||  | ||||||||||| |||||||| || |
tgatagtgagtggtatgaaacgttcttatactgaattt---tggatttttaacttggttttgaatttgacattgtttt--ctctttttaacacattgtgacatagGTTAGTGCCTCATATGAGCAGGCTCTGGTGGATGCACGCAAGATTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAAACAAAAG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 2
----cttcatgtgatat--aatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
      |   ||| |||  |||| || | | | |||   |  |  ||||||   ||   |       ||     ||||   |   || | | | ||  ||||||||||||||||||| ||||||||||||||| ||||||| || ||||  ||||| || || |||||| |||| ||  | ||||||||||| ||||| || || |
gtgatattgggtggtatgaaatattcttgtactaaa---atttggatttttgacttggttttgaatttgacaatgttt---tctcttttaacacatcgtgacatagGTTAGTGCCTCATATGAGCAGGCTCTGGTGGATGCACGCAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
cttcatgtgatataatactcgtttgcgaaat--gcagataa-atttttagtttacataccctactgttctggtt-----ttaattgattgt-gatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
           |||||  | | ||| | | |  |  ||||| |  | |    || |  || |  |  |   |||     ||| ||| || | |||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||  || || || || |||||| |||||||  ||||||| || ||||| || || || |
---------ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: PP1S134_165V6.1 (Physcomitrella patens), 3'ss of exon 3
cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAG---CAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG---------------------
              | | |  ||   || |  ||  | ||  |    ||| || |   ||| |||   |  |||||  | || ||| |     || ||   || |||| |  | || |   ||||||||  | || ||||| |||||||| || ||||| ||||||||||||||||| ||||| |||||||| || || || |                     
--------------aaatttattgatgata-acatttgaaaat---atttgcaaata-tacagttggtggattaatcaagtgcgatttg----gatattcctt-gtgctttctgtgcgatgcagGCTCTTGTTGAGGCTCGGAAGCAGATAGAGCGAGAAATGGAACGATTTAAAGTGTGTGAAAAGGAAACCAAGACAAAAGCTTTTTCTAAAGAAGGCTTGG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 3'ss of exon 3
cttcatgtgatataatactcgtttgcgaaatgcagataaatttt----tagtttacataccctactgttctggttttaattgattgtgatatatgttgaca-tagGTTAGTGCCTCTTATGAG---CAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG---------------------
                          |||     |||  ||| |    || || | | |   ||   | ||||  | | | |  ||| || | |||| | | ||     |||  |  | || |    ||||| |  | || ||||| |||||||| ||  |||| |||||| ||||||||||||||||||||||||| || || || |                     
--------------------------gaaggatggattgattctctcataattgaaaaagtttag-atactggaat-agtggggtgtaatgt-tgttaatagtattcctgtgttttctttgtggtgtagGCTTTACTTGAGGCTCGGAAGCAGATAGAGAGAGAAATGGAAAGATTTAAAGTATGTGAGAAGGAAACCAAGACAAAAGCATTTTCCAAAGAAGGCCTGG

upper sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20408 (Selaginella moellendorffii), 3'ss of exon 2
cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
                                              | |||   |   |  | |   | ||||  ||  ||     ||  |||   ||||||    || ||||| |||||||| ||| ||||||| || ||||  ||||| ||||||||||||||||| ||||| || ||||| ||||| ||||| ||||
--------------------------------------------gtgattaggcagtttcttctagcgatttttttttctt----cattcgttttgatagGTAGCAGCGTCTTACGAGCAGGCGCTGGTGGATGCCCGGAAGCTCATTGAGCGAGAGATGGAACGATTCAAAGTTTGCGAGAAAGAAACGAAAACGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
                                            tgttgac  putative branch site (score: 3)
                        ttttaattgattgtga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcatgtgatataatactcgtttgcgaaatgcagataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
cttcatg
- - - - - - - - - - - - - -aaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgattg