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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgacttggtctttctgaatataatcctgatcgatgcgacgccagccggctggttgtctctgtctcatgcatgcgatctatgctgccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCTGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC

Basic information

species Zea mays
transcript GRMZM2G340224_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340224_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 3'ss of exon 6
----------------------gtaacgact-tggtctttctgaatataatcctgatcgatgcgacgccagccggctggttgtctctgtctcatgcatgcgatctatgc-----tgccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCTGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC
                        | |  |  ||   |||| |  |  | ||   |      |     |||   || |||||      |     ||     | | | ||     |    || ||||||||||||||| |||||||| |||||||| ||||| ||||| ||  || |||||||| | || |||||||| ||| |  | ||||| ||||||||||||
gtgcattttctgaaaattctgttcagctgcaatgccatttcagtttgcagtcagcagtagaacagtatcagtatgc-ggttgcaaacattcagagctgaaaaccaacgcacatttctgctgacagGTACATCACGATCGAAGAGCTCGAGCAAGCGCTGAGAGAGAAAGGGTTGATGGACGGCAGGGAGATCAAGGACATCATATCCGAAGTCGACGCCGACAAC
















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|71425328|gb|DR806616.1|DR806616
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|21481043|gb|BQ577726.1|BQ577726
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTTGAGGGAGAAAGGCCTGC
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCT-GAGGGAGAAGGGCCTGC
EST: gi|21330641|gb|BQ486022.1|BQ486022
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|71765068|gb|DR963005.1|DR963005
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|7304607|gb|AW600546.1|AW600546
EST:     GACGAGCACCTCTACNCCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|86466802|gb|DY233172.1|DY233172
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|21480881|gb|BQ577564.1|BQ577564
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|21390432|gb|BQ528481.1|BQ528481
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|87154477|gb|DY399266.1|DY399266
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|21330105|gb|BQ485486.1|BQ485486
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|21390265|gb|BQ528314.1|BQ528314
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|12046168|gb|BF728307.1|BF728307
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
EST: gi|7216885|gb|AW563007.1|AW563007
EST:     GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGG                         GTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT
genomic: GACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCT

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 13

ACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGTTCCAGTACTTCGACAAGGACAACAGCGGgtaacgactt ... gccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCTGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgacttggtctttctgaatataatcctgatcgatgcgacgccagccggctggttgtctctgtctcatgcatgcgatctatgctgccatgccagGTACATCACGATGGAAGAGCTGGAGCAAGCCCTGAGGGAGAAGGGCCTGCTGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA