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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgaaattcttcaactgaattgtccttccacattctatagctcctccatgagtatttttacactcacagtgatcaaatatgttgtttaccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC

Basic information

species Zea mays
transcript GRMZM2G102639_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 8
---atatgaaattcttcaactgaattgtccttccacattctatagctcc-tccatgagtatttttacactcacagtgatcaaatatgttgtttaccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC
   || |||||||||  |     | |    | |    | ||| || |   | |     |||| ||||| ||| | ||||  | ||| || ||     |||||||||||  |||| |||||||| || || || ||||| ||||||||||||||||| |||||||||||||| ||||| || ||||| | | |||||||||  ||
tccat-tgaaattctgaattctgactacattgcggtttactaaagttttgttccaacatattgttacaatcataatgattga-tatattcttg--tgttgacagAGAGGTTGCTAGCAGCAAATAACCCTGGTTCTCAGAAGAATAGGCCACACACTATGTTTGCAAGTGGCCCGCCTACGCAAGGGCTTGCAAATGGTGCACC
















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|78090866|gb|DV519240.1|DV519240
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|91056510|gb|EB166928.1|EB166928
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|76015741|gb|DT942911.1|DT942911
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|71319024|gb|DR796257.1|DR796257
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|87157489|gb|DY402278.1|DY402278
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGC
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGC
EST: gi|148956981|gb|EC902927.2|EC902927
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|148933043|gb|EE285938.2|EE285938
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAA-AATAGGCCACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACA
EST: gi|78124664|gb|DV543048.1|DV543048
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|50322326|gb|CO517452.1|CO517452
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGAT
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGAT
EST: gi|211005558|gb|FL032308.1|FL032308
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|89762379|gb|DY689990.1|DY689990
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACA
EST: gi|76288123|gb|DV027691.1|DV027691
EST:     TATGCTTACAAGAAAGACACGAAAGGAAGA-CGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TATGCTTACAAGAAAGACACGAAAGGA-GAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|71425499|gb|DR806709.1|DR806709
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|31355533|gb|CD439890.1|CD439890
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|71425496|gb|DR806708.1|DR806708
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|76291455|gb|DV031023.1|DV031023
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACA-TCCAGGATCTCAAAAGAATAGGTCACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACA
EST: gi|76015742|gb|DT942912.1|DT942912
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAAGGC-ACAC
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATA-GGCCACAC
EST: gi|76290093|gb|DV029661.1|DV029661
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|148930039|gb|EE285937.2|EE285937
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
EST: gi|78124734|gb|DV543118.1|DV543118
EST:     TTATGCTTACGAGAGAGACACGAAAGGAGAACGCCGTGGCACACCAGCAG                         AGAGACTGCTGGCAGCACACAATCCAGGA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGA
EST: gi|148938096|gb|EC882358.2|EC882358
EST:     TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG                         AGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA
genomic: TTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACA

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: 49 (upstream exon), 49 (downstream exon)
Score: 138

GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 50

GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 94

GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 32

GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAGgtaatgtgtt ... ccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatgagtatttttacactcacagtgatcaaatatgttgtttaccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC
                 cactcac  putative branch site (score: 32)
                               aaatatgttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgaaattcttcaactgaattgtccttccacattctatagctcctccatgagtatttttacactcacagtgatcaaatatgttgtttaccattgacagAGAGACTGCTGGCAGCAAACAATCCAGGATCTCAAAAGAATAGGCCACACACAATGTTTGCAAGTGGTCCGCCGACCCAAGGTCATCCAAATGGTGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG