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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

Basic information

species Zea mays
transcript GRMZM2G157621_T02
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
-agtg-attaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatc-tatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
 ||     ||||| ||   ||       |     | |     | |  |  | ||   |||   |  |   || |||  |||||||||| | | | | | |||||||||||| || |||||||||||||| |||||||| || || |||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctttttt--ccacttgtttcacaaacat-agttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
agtgattaattgtccgagtaaccgactagg-ggtcgactagtcgcctggtct--tcgaccaggcgacttga--aatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
 ||||   ||| ||    ||   |  ||   |       |      | ||    | || || || |  ||   |     |  || | || |    || |    |||| || ||||| |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
-gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaattgtaattact--ttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctg-gtcttcgaccaggcgac-ttgaaatcattggt------tctgatcat--ctattt--gccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
  || |  ||| ||    ||   |  |       ||| ||| |      | ||  |  ||  ||  || | |||||  ||       || ||  |   || ||  |    |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
gttggtagattttctttttagttgctttaaa--tgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
agtgattaattgtccgagt--aaccgactagg-ggtcgactagtcgcctggtct--tcgaccaggcga--cttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
 ||||  |||  |   | |  |   |  ||   |       |    | | ||    | || || || |  | || |     |  || | || |    || |    |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
-gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattact--ttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
agtgattaattgtccgagtaaccgactaggggtcgactagtcg--cctggtcttcgaccaggcgacttgaaatcattggt------tctgatcat--ctattt--gccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
  ||||  ||| ||    ||   |  |       |||| || |  |    | ||        |   ||  ||||||  ||       || ||  |   || ||  |    |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
gttgatagattttctttttagttgctttaaa--tgacttgtggaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
--------------------------------------------------agtgattaattgtccgagtaacc-----gactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
                                                  | ||  ||  ||   || |   |      | || ||    |    |   ||  |    | |  |      |   |||  ||  |  | | | ||||||    ||||| || || || ||  | || ||||| || ||||| || || || || |||||||| || || |||||||| ||||| ||||| ||||||||||||||||
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatc--tgaatgaggtta-ctattt--ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctg-atcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
                                               ||||  |     |  | |||   |  ||  || |  | |   | | |    ||||| ||||  ||  || |  | |||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||||| || |
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
                                          | |||    |     |   |  ||    |  || ||       |||||| || |  |||| ||||  ||  || |  | |||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||||| || |
------------------------------------------gtctgtgtgtttgttatttgcttttt--ttctttgtctaacgaatctatatggc--agCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
                                ttctgat  putative branch site (score: 3)
                                             tttgcccc  putative PPT
                      aaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT