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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcccaacaagaccctcgagttccatctccacggtatgcacgcacggacggacgctggagctccttaactgcgagtgggtctgtctgacactggagctcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT

Basic information

species Zea mays
transcript GRMZM2G470499_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470499_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g54700.1 (Oryza sativa), 3'ss of exon 2
gtacgtgcccaacaagaccctcgagttccatctccacggtatgcacgcacggacggacgctggagctcctta-actgcgagtgggtctgtctgacactggagctcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT
                              |    ||    ||| || | |      |  ||  ||   | |  ||| |  | | |  | |||||||  | | | ||| || |   |||| || ||| ||||| |||||||||||||| ||||||||| ||||||||| ||||| || |||||||||||||| |||||||| ||||
-----------------------------gtaagtacttgctgc-cggatgatgtaccattgttgcgtgtaatgctggggcttgcttgggctgacacgagtggttggtttctg---cagGTAGCGGCCGGCCGGCGCTGGACTGGCCGCGGCGGTGGAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCGTATCTGCACGAGGACT
















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|101381709|gb|EB812912.1|EB812912
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|148995866|gb|EE035102.2|EE035102
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|149104235|gb|EE289671.2|EE289671
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|94477995|gb|EB706953.1|EB706953
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|71771807|gb|DR969744.1|DR969744
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|148959212|gb|EE010655.2|EE010655
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|76914139|gb|DV165421.1|DV165421
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|148987250|gb|EE031085.2|EE031085
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|94474665|gb|EB703623.1|EB703623
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|78087049|gb|DV515442.1|DV515442
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|71763339|gb|DR961276.1|DR961276
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|50334733|gb|CO529859.1|CO529859
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|148987251|gb|EE031086.2|EE031086
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|148959211|gb|EC905317.2|EC905317
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|78124341|gb|DV542725.1|DV542725
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
EST: gi|71423642|gb|DR806109.1|DR806109
EST:     TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGA                         GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG
genomic: TCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCG

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 9

TCCGCGCCGAGGTGGAGATCATCAGCCGCGTGCACCACAAGAACCTCGTCTCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT


Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 1

TCCGCGCCGAGGTGGAGATCATCAGCCGCGTGCACCACAAGAACCTCGTCTCCCTCGTCGGCTACTGCCTCTACGGCGAGCAGCGGCTGCTCGTGTACGAgtacgtgccc ... tcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctggagctccttaactgcgagtgggtctgtctgacactggagctcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT
                              gtctgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgcccaacaagaccctcgagttccatctccacggtatgcacgcacggacggacgctggagctccttaactgcgagtgggtctgtctgacactggagctcggtatcagGGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA