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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggttttgtactctccactcctaattgtaagtcgttttggcttttctataatctatgttcataccttttactatgtacctagacaca...

Basic information

species Zea mays
transcript GRMZM5G835213_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 4
TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggttttgtactctc-cactcctaattgtaagtcgttttggcttttctataatctatgttcataccttttactatgtacctagac-aca--
||||||||||||||  ||||||| |||||||| |||| ||||||| | |||||| |||| ||||| || |||||| ||||||| ||| | |  | | ||| | |   |    ||| |   | |  |||||  ||| || | | | || |||  || ||||  ||||  |||| |  ||   
TCATCCTTTGGTTTTGTTGACTATTATGACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtatttcaatactatagtattataatatatataaattctaat-attttgcttttcctcttaac-attttccaacattttcttatgatcctacattaccag

upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 4
TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggttttgtactctccactcctaattgtaagtcgttttggcttttctataatctatgttcataccttttactatgtacctagacaca
||||||| ||| |||||| | |||| ||| ||||||| |||||| || || || |||||||||||||| || || ||||||||      ||| | ||    | |    |   ||||| |  || |||||   | |  | | ||||  |  || | ||  |                 
TCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagt-----gttgctgttaagatttatgtta--aattg-atttcattttg---tgttcaaattctaattcaatgctttgcag----------------

upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 4
TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggttttgtactctccactcctaattgtaagtcgttttggcttttctataatctatgttcataccttttactatgtacctagacaca
||||||| ||| |||||| | |||| ||| ||||||| |||||| || || || |||||||||||||| || || ||||||||      ||| | ||    | |    |   ||||| |  || |||||  | ||||| | | ||  |  || | ||  |                 
TCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagt-----gttgctctttagatttatgtta--aattg-atttcattttg--tattcta-attttaattcaatgctttgcag----------------

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|71436375|gb|DR817425.1|DR817425
EST:     GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     GACCGCAGATATGCTGCACTGGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|22546594|gb|BU098905.1|BU098905
EST:     GCTGCACTGGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|22545671|gb|BU098030.1|BU098030
EST:     GACCGCAGATATGCTGCACTGGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|29544652|gb|CB605032.1|CB605032
EST:     GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|113834860|gb|DW954944.1|DW954944
EST:     ACCGCAGATATGTCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCC
genomic: ACCGCAGATATG-CTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCC
EST: gi|71317247|gb|DR795307.1|DR795307
EST:     GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
EST: gi|5268356|gb|AI770320.1|AI770320
EST:     GACCGCAGATATGCTGCACTGGCAATTTTATCTCTCAATGGCAGACAACT                         GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA
genomic: GACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGA

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), 49 (downstream exon)
Score: 551

TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 389

TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 441

TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 749

TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttt ... caaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggttttgtactctccactcctaattgtaagtcgttttggcttttctataatctatgttcataccttttactatgtacctagacaca

- - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - TGCTGC