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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcctcctgctgtttgcgtgttgcttggttttggtttgttggcttctaactcaggggtcattgagggtgatgtacccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG

Basic information

species Zea mays
transcript GRMZM2G068392_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 1
gtaaggcctcctgctgtttgcgtgttgcttggtt--------------ttggtttgttggcttctaactc--aggggtcattgagggt-gatgtacccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG
|| ||   |||||  | |  || ||| || || |              |||| ||  ||  ||  | ||   | ||||| ||| |||| |  | |       ||||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||||| ||||  || | ||||||  | ||||| ||||||
gtgagatttcctgaagatatcgcgttactaggctctgtgtattcgtatttggcttactgtttttcagctttgatgggtcgttgtgggttggggaattggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAGGGGGTCCCTGACGGCGCCGCCGTCCGTCCTACTGTGTGGAAG
















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|78076514|gb|DV504948.1|DV504948
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170262|gb|FL097991.1|FL097991
EST:     GCCTACG-CGGAATTTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: GCCTACGCCGGAA-TTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170259|gb|FL097988.1|FL097988
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGTGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170268|gb|FL097997.1|FL097997
EST:     CGCCTACGS-G-AATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211168574|gb|FL097971.1|FL097971
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170258|gb|FL097987.1|FL097987
EST:     GCCTACG--SGANATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: GCCTACGCCGGA-ATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211168582|gb|FL097979.1|FL097979
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170254|gb|FL097983.1|FL097983
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170266|gb|FL097995.1|FL097995
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211168573|gb|FL097970.1|FL097970
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211166904|gb|FL097963.1|FL097963
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170264|gb|FL097993.1|FL097993
EST:     GCCTACG-C-GANATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: GCCTACGCCGGA-ATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|44681890|gb|CK786938.1|CK786938
EST:     CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
EST: gi|211170257|gb|FL097986.1|FL097986
EST:     CGCCTACG-CSSAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG
genomic: CGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAG

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: 68

CATCCCGACGCCCAAATCCATGGCGAGCTCGCCGCGATCTCCTCCGCCGGCGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

CATCCCGACGCCCAAATCCATGGCGAGCTCGCCGCGATCTCCTCCGCCGGCGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 69

CATCCCGACGCCCAAATCCATGGCGAGCTCGCCGCGATCTCCTCCGCCGGCGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

CATCCCGACGCCCAAATCCATGGCGAGCTCGCCGCGATCTCCTCCGCCGGCGCCTACGCCGGAATTCGAGATCTCTCGGCAGTCCCGCCTCTTTGTGGCGgtaaggcctc ... acccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtttgttggcttctaactcaggggtcattgagggtgatgtacccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG
               ttctaac  putative branch site (score: 54)
                                            tacccttct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcctcctgctgtttgcgtgttgcttggttttggtttgttggcttctaactcaggggtcattgagggtgatgtacccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG