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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC

Basic information

species Zea mays
transcript GRMZM2G156956_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 13
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtg---agaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
         |       ||  |     |   | ||||  |  |  | |  |  |    | |    ||||| | ||    | | |||||| |  |  ||| | ||   |||||||||| || ||||||||||||||||| ||||||||||| || ||||| || || || |||||| | || || |||||||  ||||||||||||||||| |
---------ttaaaaagtatttctgccctgtagagtactgccagttttcccctggc--attttctaattgaaagtatgcataggattaattggacttgacatttgc-tgcagACATTTAATGGCAAGAAATGGGAGAAATTCAATAGTGAAAAGGTGGCGTCGCTCGCATACGCCCGGATTCAAGGAAGGAGTGCTTTGATTGCTCATTTTC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
                 |   | |||        |    |    || ||| || | | | |   |  ||     ||   |    ||||| |      | |  | ||||| | ||  | || || |||||||||||||| |||||||| ||||| || |||||||| || ||| |||| || ||||      || | |||||||||||||
---------------gttgtttggattttcttatgctttgagctatctatgtactatgaattttgggttcctcatgttgatgg-aactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
----------gtatgttcctgtgcccat-accttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatg---tgagaagattaactatagctgatacttctgt----gcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
          | |  |     || | || |   ||||  |||  |  |     ||  | ||    || |    || |     ||    ||     ||  |||  |||| ||  | |  |    ||||   ||| | || |||||||||||||| ||||| |||||||||||||||||||| || || ||  | || || || |     ||| | |||||||| ||||
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaa-acttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
gtatgttcct----gtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagatta-acta------tagct---gatacttctgtg-cagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
||||| |        ||   ||  |     |  |||  |      ||  ||||   |  | |  | || |     | |     | | |  ||||      || ||   ||| | | | || |||   ||||| || |||||||||||||| ||||| |||||||||||||||||||| || || ||  | || || || |     ||| | |||||||| ||||
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaaga--ttaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
||||   | |       ||||||  ||      | |   | | |  || | |  ||   ||  ||||    | |  | |||   ||   || |  |   |   ||   ||| |||||||||| ||||||||||| |||||||| || ||||| |||||||| ||||| || |   | || ||||| |     ||| | ||||| |||||||
gtataagctt-----tgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
  |  | ||    || | |      |   ||  |  |   ||   | | || ||||       |  |||   |    ||| |  |  || | |  ||   | || |||| ||||||| || ||||||||||||||||||||||| || || |||||||||||||| || ||| | || ||||||| |   ||| | ||||| |||||||
--aaatacc---acctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaat---tttg-gcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgt-gcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
                                    ||  ||  |  ||    |    || | ||    ||      || |  ||   || |    |    || |  || ||   | | | |   |  |   |  | | |  ||| ||||||| || || || |||||||||||||| |||||||| |||||||| ||||| || ||  |||| || ||||  |  ||| | |||||||||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaag-gaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgt-gcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
                                    ||| ||  |  | |  |     || | ||    ||      || |  ||   || ||   |    || |  || ||   | | | |   |  |   |  | | |  ||| ||||||| || || || ||||||||||||||||||||||| |||||||| ||||| || ||   |||  | ||||  |  ||| | | |||||||||||
gtttgaatccatggattgtaatataattatacttaatat-ttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC

upper sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
                       | |  |||  |  ||| || |  | || |  |   ||    || |||| | |   || | |    ||   |  |  |      ||||| ||||| |||||||||||||||||||| || || ||||| |||||||| || ||||||||  | ||||| || | |  |||  |||| || || ||||
-----------------------gttctctgtgaaaaagagagaggagattt--tcctac----gacttggttct---aaaacttgtcattctttgtttt----cacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71332238|gb|DR803044.1|DR803044
EST:     ATGCATTCATCAATATGACGGATCCCCAGCAGATAGTTCCTTTTTCCAAG                         ACATTCACCGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
genomic: ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
EST: gi|60394908|gb|DN227777.1|DN227777
EST:     ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAG                         ACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
genomic: ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
EST: gi|5915119|gb|AW052760.1|AW052760
EST:     ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAG                         ACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
genomic: ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
EST: gi|67012060|gb|CO440809.1|CO440809
EST:     TGCATTCATC-TTATGACGGATCCACAGCAGATAGTTCCATTTTACAAG                         ACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
genomic: TGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
EST: gi|71332239|gb|DR803045.1|DR803045
EST:     ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAG                         ACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
genomic: ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
EST: gi|32851005|gb|CD990686.1|CD990686
EST:     ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAG                         ACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA
genomic: ATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 110

AATAAATGTAACGTGGGATATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 91

AATAAATGTAACGTGGGATATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

AATAAATGTAACGTGGGATATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 276

AATAAATGTAACGTGGGATATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAGgtatgttcct ... ttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
                                          tacttct  CT-rich tract
                           attaactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA