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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagttattgctctatatattcttctcagtcatctggatgttagcatttcaatttgttgagtgtggtaataagtttctactccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 6
gtaagagtt---attgctctatatattcttctcagtc----atctggatgttagcatttca-----atttgttgagtgtggtaataagtttctactccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG
||| || ||   |||   ||||  ||| ||  ||       |     |  |  | | |        | ||||      | | |||||  || | ||  || ||||||||||||||| ||||||||  |||||||||| ||||| ||||| | |||||| ||||||||||| || |||||||| |||||||| |||||||||
gtaggatttaccattctcctatggattttttccatctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 7
--------gtaagagttattgctctatatattcttctcagtcatctggatgttagcatttcaatttgttgagtgtggtaataagtttctactccattca-agGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG
          |  ||||||| || | | |||| || |   | ||  |  |   ||  |||  |       | | |  | |||  | ||| |||| | || |||||||||||||||||||  |||| |||||| |  | || ||   ||||||||||||||||||||| ||||| |||||||||||||||||||| |||
ttctcttaaaagaagttatttcttt-tttatt-ttgtatttgattcgttttcaagtcttttcacactggaattatcttcatatatatctgctccttacacagGTTGCATGTGCATTGCTTATGGCGGGTGAGGATCTAGACAAAAATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
gtaagagttattgctctatat---attc-ttctcagtcatctgg--atgttagcattt-caatttgttgagtgtggtaataagtttctactccattca-agGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG
       || ||  | |||||   |||| || ||| |  |||    |   | | || | | || ||||   | |  | ||| || ||| |||| | || |||||||||||||||||||  |||| |||||| |  | || |||  ||||||||||||||||||||| ||||| |||||||||||||||||||| |||
-atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatatactatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG

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|76293424|gb|DV032992.1|DV032992
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|76293423|gb|DV032991.1|DV032991
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|78117581|gb|DV535968.1|DV535968
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|149100778|gb|EE186872.2|EE186872
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|211448759|gb|FL324438.1|FL324438
EST:     CCGCCGCATCGTTCAGTACAAGACAGCTTTAT-ATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGG
genomic: CCGCCGCATCGTTCAGTACAAGACAGCTT-ATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGG
EST: gi|149100779|gb|EE186873.2|EE186873
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTG
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTG
EST: gi|60339232|gb|DN206205.1|DN206205
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|60359240|gb|DN226213.1|DN226213
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|60355012|gb|DN221985.1|DN221985
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|148951737|gb|EC897492.2|EC897492
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|148950117|gb|EC895653.2|EC895653
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|60341646|gb|DN208619.1|DN208619
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|148964885|gb|EE015747.2|EE015747
EST:     CCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: CCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|71310911|gb|DR791758.1|DR791758
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAA-CTTTTGT-GA
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTT-GTTGA
EST: gi|211504975|gb|FL314285.1|FL314285
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|71310909|gb|DR791757.1|DR791757
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|148964886|gb|EE015748.2|EE015748
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|78117582|gb|DV535969.1|DV535969
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
EST: gi|60353036|gb|DN220009.1|DN220009
EST:     ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT
genomic: ACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGAT

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), 49 (downstream exon)
Score: 173

TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 557

TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 561

TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 284

TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagtta ... tccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgttagcatttcaatttgttgagtgtggtaataagtttctactccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG
                                      tttctactccattc  CT-rich tract
          atttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagttattgctctatatattcttctcagtcatctggatgttagcatttcaatttgttgagtgtggtaataagtttctactccattcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC