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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggccaaatcagtagagttgcgcttgttttctgtggcactgtttatctaagttctgttgcaatggaggtctacagtttcagtcgttctgaattctgatccgtgactgcctctgttgcag

Basic information

species Zea mays
transcript GRMZM2G171688_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 5'ss of exon 8
GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggccaaatcagtagagttgcgcttgttttctgtggcactgtttatctaagttctgttgcaatggaggtctacagtttcagtcgttctgaattctgatccgtgactgcctctgttgcag
||||||||| | |||||| |||| |||||||| | |||||||||||| || || || ||  |||||||||| |||||||| || || || || ||||||||||||      ||  |   ||   ||   |    | | | |   |  | || | | ||||  |   ||| ||   |  | |||    | |    ||  ||  |||                   
GTCTTTCCACTTGTCAAGATCGAAAAATTTGAAGTTGTTGCCAAGAAAATTTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactattgaactatgtgaa--gcatatagcatttattgtgtt--tgatttcaattctaatcatatgaagcagtgtaatttg---cataagaaagccttttcccc-----------------
















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|87155844|gb|DY400633.1|DY400633
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|211414533|gb|FL447521.1|FL447521
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATAACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|148973606|gb|EE024714.2|EE024714
EST:     AGCTGGGTTTTCACATATCATGGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
genomic: AGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|78023468|gb|DV491855.1|DV491855
EST:     ACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: ACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|78544321|gb|DV621819.1|DV621819
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|211312130|gb|FL216566.1|FL216566
EST:     CTTCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|51592897|gb|CV072043.1|CV072043
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATAACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|32846971|gb|CD986652.1|CD986652
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGT
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGT
EST: gi|211517427|gb|FL458392.1|FL458392
EST:     YTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|5566904|gb|AI881815.1|AI881815
EST:     TGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: TGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|211312129|gb|FL216565.1|FL216565
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|101390015|gb|EB816939.1|EB816939
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|211517428|gb|FL458393.1|FL458393
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|67021585|gb|CO450334.1|CO450334
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATAACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|16377735|gb|BI992091.1|BI992091
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|211414534|gb|FL447522.1|FL447522
EST:     CTCCAAGGCCATGACAGCAGCTGGGATTTCACATATCATCGACATAACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC
EST: gi|32929715|gb|CF034527.1|CF034527
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGT
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGT
EST: gi|213173866|gb|FM192224.1|FM192224
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GGAATACAATA
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATA
EST: gi|20208385|gb|BQ134474.1|BQ134474
EST:     CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAG                         GTAATACAATAGGAAAACGGTACGCAAGGACGGACGAGATTGGTGTCCCCC
genomic: CTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCC

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), 48 (downstream exon)
Score: 236

GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCCTGGCGATCACGGTTGATCACACCACGAGCGTGACGGTGCGCGATCGTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 174

GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCCTGGCGATCACGGTTGATCACACCACGAGCGTGACGGTGCGCGATCGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCCTGGCGATCACGGTTGATCACACCACGAGCGTGACGGTGCGCGATCGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggcc ... tctgttgcagGTAATACAATAGGAAAACGGTACGCAAGGACGGATGAGATTGGTGTCCCCCTGGCGATCACGGTTGATCACACCACGAGCGTGACGGTGCGCGATCGTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggccaaatcagtagagttgcgcttgttttctgtggcactgtttatctaagttctgttgcaatggaggtctacagtttcagtcgttctgaattctgatccgtgactgcctctgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG