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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcaggtgtaccataccgtgacaccgagcgtctccaagtgatttgtgaatataaaggtcacatttttttttgacatcttcgctcttcaatttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG

Basic information

species Zea mays
transcript GRMZM2G099101_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099101_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 3'ss of exon 1
-tgtcaggtgtaccataccgtgacaccgagcgtctccaagtgatttgtg-aatataaaggtcacatttttttttgacatcttcgctcttcaatttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG
    ||   |||  | |       |       |     | | || |||  ||  ||||| |||||||||  |   || ||  |  |  |  ||||||||||||||| |||||||||||| |||||||| | |||||||| |||||||| |||||||||||||| || || || || |||||| |||| ||||| || || ||
gatccatccgtaa-agattacaggagtttatctagaagaataatatgtccaacttaaagatcacattttgatggtacttcc-catttgtgtatttgctgcagCTGGAAAGCTTCCGAAGAACAACAATGTGCATTGGCGTGGTAACTCGTGCATGAAGGACGGACTCTCGGATCCGGCAGTCGGGCGCAGCCTCGTCGGAGG

upper sequence: GRMZM2G099101_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15004 (Selaginella moellendorffii), 3'ss of exon 1
tgtcaggtgtaccataccgtgacaccgag-cgtctccaagtgatttgtgaatataaaggtcacatttttttttgacatcttcgctcttcaatttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG---
      ||   |     | |  | || ||  |    ||  | |||| |     || |  ||      |   ||| |   |||  | |||  ||   ||||||||||||||| ||||||||||||||  ||  ||   | || || ||| ||||| | || ||  |    || ||||   ||    | | | || | || ||   
------gtaagctcgctcatagctcctaggtggtagcatttcatttct---cttagaactctttcgctaagttggc-ctttcttttttcgtttctttgcagCTGGGAAGCTCCCGAAGCACAACAACGTATCTTTTAGAGGCAATTCTGGCATGCAAGATGGAGTG---GATCCTGGGATCCACGGGAACTTGATCGGGGGCTA

upper sequence: GRMZM2G099101_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ37685 (Selaginella moellendorffii), 3'ss of exon 1
tgtcaggtgtaccataccgtgacaccgag-cgtctccaagtgatttgtgaatataaaggtcacatttttttttgacatcttcgctcttcaatttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG---
      ||   |     | |  | || ||  |    ||  | |||| |     || |  ||      |   ||| |   |||  | |||  ||   ||||||||||||||| ||||||||||||||  ||  ||   | || || ||| ||||| | || ||| |    || ||||   ||    | | | || | || ||   
------gtaagctcgctcatagctcctaggtggtagcatttcatttct---cttagaactctttcgctaagttggc-ctttcttttttcttttctttgcagCTGGGAAGCTCCCGAAGCACAACAACGTATCTTTTAGAGGCAATTCTGGCATGCAAGATGGGGTG---GATCCTGGGATCCACGGTAACTTGATCGGGGGCTA

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|26456242|gb|CA827825.1|CA827825
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|88757083|gb|DY541224.1|DY541224
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|88752247|gb|DY536388.1|DY536388
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGC
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGC
EST: gi|71426408|gb|DR807458.1|DR807458
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|71769001|gb|DR966938.1|DR966938
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|20208085|gb|BQ134174.1|BQ134174
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATCGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|50337315|gb|CO532441.1|CO532441
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|148932216|gb|EC875712.2|EC875712
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|101387306|gb|EB815669.1|EB815669
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|76285583|gb|DV025151.1|DV025151
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
EST: gi|50334088|gb|CO529214.1|CO529214
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCG
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCG
EST: gi|211231953|gb|FL399561.1|FL399561
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGC
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGG-AAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGC
EST: gi|148980726|gb|EE027316.2|EE027316
EST:     CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGAT                         CTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA
genomic: CTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCA

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: 47 (upstream exon), 43 (downstream exon)
Score: 51

ATCGCCAAGGCCATCCCCAGGCGGCACCGCCCGCTGCCACCGCCCGACGACTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG


Block sizes: 29 (upstream exon), 40 (downstream exon)
Score: 6

ATCGCCAAGGCCATCCCCAGGCGGCACCGCCCGCTGCCACCGCCCGACGACTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG


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

ATCGCCAAGGCCATCCCCAGGCGGCACCGCCCGCTGCCACCGCCCGACGACTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG


Block sizes: 36 (upstream exon), 43 (downstream exon)
Score: 2

ATCGCCAAGGCCATCCCCAGGCGGCACCGCCCGCTGCCACCGCCCGACGACTACACCGTCGCGCTGCACAAGGCGCTCATGTTCTTCCATGCCCAGAGATgtgagtagtt ... tttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatataaaggtcacatttttttttgacatcttcgctcttcaatttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG
                       ttttgac  putative branch site (score: 2)
                 atttttttttgacat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcaggtgtaccataccgtgacaccgagcgtctccaagtgatttgtgaatataaaggtcacatttttttttgacatcttcgctcttcaatttgctgcagCTGGGAAGCTTCCGAAGCACAACAATATACATTGGCGCGGTAACTCTTGCATGAAGGACGGGCTTTCTGACCCTGCAGTCAGGCGAAGCCTGGTTGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - -ccatacc
- - - - - - - - - - - - - - - - - - - -tgatttg