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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_T01
intron # 11
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 41 (downstream exon)
Score: 108

GAATATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtgatt ... cctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 90

GAATATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtgatt ... cctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA


Block sizes: 42 (upstream exon), 31 (downstream exon)
Score: 79

GAATATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtgatt ... cctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 120

GAATATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtgatt ... cctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA




 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