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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

Basic information

species Zea mays
transcript GRMZM5G816636_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtcagtgattttctctggtatcatgcttgctttacg------gcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
||||||    |  | |  | |  |  | || |  |       ||  || ||    | | |||| |||||||||  | |  | ||| ||||||||| || |||||||||||||||||||||||||| || ||||| ||||| || ||||||||| | || ||||||||||| ||||||||||||||||||||
gtcagtcgcctcttttattctacttttagcatcccaagctttgcttgatttcactgtaacaaa-atctcagatcttatgcttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
------------------------------------------gtcagtg-attttctctggtatc-atgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                                           |  ||| || |||  |   ||  |||  ||| || |     |||  |     |||||  ||  ||  |  | |||   |    ||||||||||||| ||||| || ||  |||| ||||| || ||||| || || ||||||||||| || ||||| ||||  || |||||||||||||| || ||
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
---------------------------------gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                                 ||  |    |||   |    | |||  ||| || |     |||  |     |||||  ||  ||  |  | |||   |    ||||||||||||| ||||| || ||  |||| ||||| || ||||| || || ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcat-tttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------------------gtcagtgattttct----ctggtatcatgcttgctttacggcaa--gaattgctagcatcaaatatctcaga---tgctgttatccta-ctgc-agATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                                                                                | |  | |||| |     | |  | |   ||   | |    ||  || ||    ||   |      | |||   || ||||||  || |||| ||||||||| |||||||| || || ||||| ||||| || || || ||||||||||| ||||| || ||||| ||||  |||||||| || ||||| || ||
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgc-ctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
------gtcagtgattttctctggtatcatgcttgctt-------tacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
           | |   |   ||| || ||   ||           || | ||  |    | ||   ||   |      | || ||    |  | |||||||||| || ||||| || || ||||| ||||| || ||||| || || ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------gtcagtgattttctctggtatcatgcttgctttacggcaa--gaattgctagcatcaaatatctcagat--gctgttatccta-ctgc-agATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                                                                         |||  | |||| |    | | |   ||   | |    ||   | ||     ||||          | |  | |||| |  || |||| ||||||||| |||||||| || || || |  ||||| || || |||||||||||||| ||||| || ||||| ||||  |||||||| || ||||| || ||
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
-------gtcagtgattttctctggtatcatgcttgctt---tacggcaagaattgctagcatcaaatatctcagatgctgttatcc-tactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
          | | |   |   ||| || |||  ||       || | ||| |    | ||   ||   |      | || || ||  |  | |||||||||| || ||||| || || ||||| ||||| |||||||| || || ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtgattt----tctctggta------tcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgtta-tcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
|||||||| ||    | | || |       | ||  || ||||  |    |  ||  || ||  | || ||| || |    | | |  |  ||||||||| || |||||||| ||||| |||||  |||| || ||||| ||||| ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagat-tctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------gtcagtgattttctctggtatca--tgcttgctttacggcaagaattg-------ctagcatcaaatatctcag---atgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                                                                |||  |  ||| | |||     |  ||||| | ||  ||| |             || ||||   |||   | |   ||  ||  ||  | |||||||||| ||||| ||||| || || ||||| ||||| || || || ||||||||||||||| |||| ||||| || |   ||||||| || ||||| || ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                 ||  | | | || ||| |        ||||     ||   | |||||  |  || |       | ||||||||||||| ||||| || || || |  ||||||||||| || |||||||||||||| || || |||||||||| | |||| ||||| |||||||| ||
-------------gtcagtgcc-tacgtgtttttc--------ttgccttt-tcttttctctcaacttttgat------tttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
lower sequence: EFJ23976 (Selaginella moellendorffii), 3'ss of exon 11
gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                       |   ||| | |||  |    ||  |  | ||   | ||||  |   | | ||  |    ||||||||||||| ||||| || || || |  ||||||||||| || |||||||||||||| || || |||||||||| | |||| ||||| |||||||| ||
----------------------gtcagtgcct-acg--agtttttcttgccttctcttttctctcaacttttgatttt----cagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA
                                         ttatcct  CT-rich tract
                     atcaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA