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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggtccggtctttgttcgagagggaggagctggaatgcacgtccggtgtgggcctgtaaatggcttctgattcctcgatctggcctgggttttgcag

Basic information

species Zea mays
transcript GRMZM2G064753_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064753_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 5'ss of exon 2
GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtg-agatgg---------------tccggtctttgttcgagagggaggagctggaatgcacgtccggtgtg---ggcctgtaaatggcttc--tgattcctcgatctggcctgggttttgcag
|||||||||||||||  |||||||||||||||||||||||||||||||| ||||| |||||||| | ||| |||||||||||| |||||                | || | ||| ||          | | |||| |     |||  | ||   |  ||| |||||| ||   |||||   ||||||| |   ||||| ||||
GGGACAAGCCGGCGACGGTGGAGGACGTCATGCCCATCGCCACGGGGCTGGAGCGCGAGGAGCTCGCGGCGGAGCTCAAGgtggagatgcctatgccttttttttttcgtttttttttttgcttcttcgggttggagtattgctcctttttgtctgttctggaaatgggtttcgtgatttgccgatctgtctgtggtttcgcag
















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|211282257|gb|FL038859.1|FL038859
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|60341353|gb|DN208326.1|DN208326
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|71446669|gb|DR827719.1|DR827719
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|211158395|gb|FK955819.1|FK955819
EST:     TGCCCATCGCCACGGGNCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|211235602|gb|FL469489.1|FL469489
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAA
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAA-Ggtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAA
EST: gi|211161585|gb|FK955846.1|FK955846
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|60343233|gb|DN210206.1|DN210206
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|60340030|gb|DN207003.1|DN207003
EST:     GAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: GAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|24763662|gb|CA398833.1|CA398833
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|211282259|gb|FL038861.1|FL038861
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|60353974|gb|DN220947.1|DN220947
EST:     CTCGAGCGAGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: CTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|24768560|gb|CA403689.1|CA403689
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|5108358|gb|AI740071.1|AI740071
EST:     GAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAAAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: GAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|44901526|gb|CK828071.1|CK828071
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGATATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|101401431|gb|EB822393.1|EB822393
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|60398986|gb|DN231802.1|DN231802
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
EST: gi|78026436|gb|DV494823.1|DV494823
EST:     CCATCGCCACGGGGCTCGAGCGAGAGGAGCTGGAGGCCGAGCTCAAG                         GGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG
genomic: CCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG

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), 44 (downstream exon)
Score: 143

GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATCCCCTGGTCGGCCCCTTCGGTACCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAGgtgagatggtccggtctttgttcgagagggaggagctggaatgcacgtccggtgtgggcctgtaaatggcttctgattcctcgatctggcctgggttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA