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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcggagaatcaacacaaatgtttttcaattttttaatgtttttatttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG

Basic information

species Zea mays
transcript GRMZM2G056462_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
atgcggagaatcaacacaaatgtttttcaatttttta---atgtttttatttctaag--cttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG
     |   ||   |       ||||   |  |  ||    ||   || |   |||   |||| |     |  ||| | |  |||| |    |  | | ||| |||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||||||||||| || ||||| |||
-----gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG

upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
atgcggagaatcaacacaaatgtttttcaattttttaatgt--ttttatttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG
||    |    | |   |   | |      ||||||  | |   ||||| |  ||      |  | |  |  | |||  ||       |||  |  ||  ||| || || ||||| ||||||||||||||||| || |||||||||||||| || |||||  || |||||||||| || || || |||
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgatt--gtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG

upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S93_178V6.1 (Physcomitrella patens), 3'ss of exon 6
atgcggagaatcaacacaaatgtttttcaattttttaatgtttttatttctaagcttgctaa-ataattcttccttgtttttgtgcaatt-tcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG
 ||       ||| | ||| | || | |  |||  |          |   | |    | |   || |     | |  ||||     | |  ||   ||  |||||| ||||| || ||||||||||| ||||||||||| ||||| ||| | || |||||| | |||||||| || || || ||||||
ctgtaccttttcagcgcaa-tattgtgct-tttgctgcctcggaagtacatgaaacggttgggatgagctaacatcattttcactgactcatcttgttgcagATGAGTATGTTATGTGCAATGGTTGTAAGAGTCCGGACACCATCCTTACCAAGGAGAACCGTTTGTTCTTTCTTCGTTGTGAGCAG

upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S386_20V6.1 (Physcomitrella patens), 3'ss of exon 6
-atgcggagaatcaacacaaatgtttttca-attttttaatgtttttatttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG
  |||      ||| ||    |||| | || | | |||  ||     | |   ||| ||   ||||  |  |    ||| ||| || |   ||   ||  ||||||||| || || ||||||||||||||||||||||| || || ||| | || |||||  |||||||||| || || || ||||||
cctgcactccttcagcatgt-tgttctgcataatgttttctggaagaagtcgaaagtttcgcaaattctaataggatgtgttt-tggatcctcttgttgcagATGAATACGTTATGTGCAATGGTTGCAAGAGTCCGGACACTATCCTTACGAAGGAGAATCGGTTGTTCTTTCTTCGTTGTGAGCAG

upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ28838 (Selaginella moellendorffii), 3'ss of exon 7
atgcggagaatcaacacaaatgtttttcaattttttaatgtttttatttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG
                       || ||||| | ||    |||   |   |  | |||   |  |    |   || ||| |   | ||  |       ||||||||| || || |||||||| |||||||| || || || |||||||| ||||| |||||| | || || || ||||||||||| 
------------------gtaagttctcaatctcttttcatttccttcgtttcgtttgtctaggagaaatcatttctttat---cgatcgc-------agATGAATACGTTATGTGCAATGGCTGCAAGAGCCCCGACACTATTCTTTCGAAAGAAAACAGGCTCTTTTTTCTACGATGCGAGCAA

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|76291710|gb|DV031278.1|DV031278
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|71417947|gb|DR804264.1|DR804264
EST:     AGGAAGATTTGCACCAGAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTTTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|87155564|gb|DY400353.1|DY400353
EST:     AAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|211142063|gb|FL081585.1|FL081585
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|60349693|gb|DN216666.1|DN216666
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|29577103|gb|CB617215.1|CB617215
EST:     AGGAAGATTTGCCCCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTT
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCT-
EST: gi|60337488|gb|DN204461.1|DN204461
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|29947496|gb|CB816686.1|CB816686
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|60338551|gb|DN205524.1|DN205524
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|32933168|gb|CF037980.1|CF037980
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|32936402|gb|CF041221.1|CF041221
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|76291709|gb|DV031277.1|DV031277
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|29947331|gb|CB816599.1|CB816599
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|60339292|gb|DN206265.1|DN206265
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
EST: gi|30031975|gb|CB833826.1|CB833826
EST:     AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCA                         ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA
genomic: AGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTA

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: 165

GAGATGGGAACAAGTGGATCCCTGGATGGGCAACAAAGGTTGGTTATCAAAGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GAGATGGGAACAAGTGGATCCCTGGATGGGCAACAAAGGTTGGTTATCAAAGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GAGATGGGAACAAGTGGATCCCTGGATGGGCAACAAAGGTTGGTTATCAAAGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GAGATGGGAACAAGTGGATCCCTGGATGGGCAACAAAGGTTGGTTATCAAAGGAAGATTTGCACCAAAAAATTTCGAAGCGATACTTAGGAGATATATCAgtaagttaaa ... cgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG
           tgctaaa  putative branch site (score: 112)
                                          tttcgcttttt  putative PPT
              taaataattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcggagaatcaacacaaatgtttttcaattttttaatgtttttatttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - -caacaca
- - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - agcttgc