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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcattggctttctttctggatctgattccaccattgatctgtcacaaatctgcctctcacctgatcttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG

Basic information

species Zea mays
transcript GRMZM2G144254_T06
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 13
gtcattggctttctttc-tggatctgattcc--accattgatctgtcacaaatctgcctctcacctgatcttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG
|| ||| | |||  ||  | || |||||||   |   |  | ||||     |    | |||||  |||||||  |||||||| || ||||||||||| ||||||||||||||||| || || |||||||| || |||||||| ||||| |||||||| ||| ||||||| || |||||||
gtgatttgtttttcttgatagaactgattcaaaattttgtacctgtatttgactctcatctcatgtgatcttccttgcagTCGGCTTGCTCCATGTCACTTGGCCTTGGGGAGGAGACCATCAGCGCTTCATCGGTGCTTGCGATGCCGATGGTCTCCTCACGAACAACAGGGTTCAGAG
















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|60359035|gb|DN226008.1|DN226008
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|88756245|gb|DY540386.1|DY540386
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|93281607|gb|EB673871.1|EB673871
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|19769516|gb|BQ034237.1|BQ034237
EST:     AAGCACAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACCCAATAAGCGCTTCG
genomic: AAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|32808432|gb|CD960666.1|CD960666
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|6056875|gb|AW091280.1|AW091280
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|88756206|gb|DY540347.1|DY540347
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|6828189|gb|AW331832.1|AW331832
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|6227147|gb|AW155676.1|AW155676
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTT
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTT
EST: gi|32792658|gb|CD944894.1|CD944894
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|60351321|gb|DN218294.1|DN218294
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|113701592|gb|EE679096.1|EE679096
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|40334752|gb|CK368822.1|CK368822
EST:     CACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: CACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|60350817|gb|DN217790.1|DN217790
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|37378198|gb|CF625769.1|CF625769
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|60356320|gb|DN223293.1|DN223293
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|19822362|gb|BQ048386.1|BQ048386
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|19770035|gb|BQ034756.1|BQ034756
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAGAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|5713925|gb|AI943910.1|AI943910
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|19822356|gb|BQ048380.1|BQ048380
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
EST: gi|60399257|gb|DN232071.1|DN232071
EST:     TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG                         TCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG
genomic: TTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCG

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: 108

AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 56

AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 38

AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAGgtcattggct ... ttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattccaccattgatctgtcacaaatctgcctctcacctgatcttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG
                                           tcttgttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattggctttctttctggatctgattccaccattgatctgtcacaaatctgcctctcacctgatcttgtttgcagTCTGCATGCTCCATGTCCCTTGGCCTTGGGGAGGACACAATAAGCGCTTCGTCCGTGCTTGCCATGCCTATGGTCTCATCAAGAACAACCGGCTTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC