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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgcagcagcagccccaaccggcttttaccgttccctccgtggtccgtgctcgtgatccgtgtattcatccgccggttcctggacctggtagcc...

Basic information

species Zea mays
transcript GRMZM2G075250_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075250_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g12800.1 (Oryza sativa), 5'ss of exon 1
CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGAC-AGCAGCCCTCCCGA-----CCCCGAGgtagcgtcgcagcagcagccccaaccggcttttaccgttccctccgtggtccgtgctcgtgatccgtgtattcatc--cgccggttcctggacctggtagcc-
   ||||||||||||||||||||||||||||||| |||||||| ||||||||||   |||||  || | | ||||| || |||| | | ||         |||||||||||    |  |        |||||   |||    | ||      | |      |  ||| | |||| || |  |  ||  ||    | |   | |  |   
---CCTCTGGGGCCTCGGCGACATCGGCGCCCAGGCCGTCACCCACTACTCCGC---CCCCGGACGCCCCCGCCACCACCAGCACCACGCCAAGAATCCTCCCGAGgtagccaatctcctatctgttcaacc---tttaggtgatctgaggattggattctcctgtggtgcgtggatgcggcctcgttgggatgttgttatagccgttc
















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|9952964|gb|BE639547.1|BE639547
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAATATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|19436539|gb|BM952949.1|BM952949
EST:     CCGCCCGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|211338922|gb|FL166540.1|FL166540
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|211196797|gb|FL166531.1|FL166531
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149029944|gb|EE286281.2|EE286281
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|91052916|gb|EB163334.1|EB163334
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149101568|gb|EE187694.2|EE187694
EST:     GCTAGCCCCGGCCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: GCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149029847|gb|EE154788.2|EE154788
EST:     GACCGTCGCGGCCCCGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: GACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149110522|gb|EE190462.2|EE190462
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|211338919|gb|FL166537.1|FL166537
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|211338920|gb|FL166538.1|FL166538
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|78026712|gb|DV495099.1|DV495099
EST:     ACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: ACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|32856691|gb|CD996372.1|CD996372
EST:     CCGCTCGCCCCGACCGTGGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149045900|gb|EE047899.2|EE047899
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149102531|gb|EE287889.2|EE287889
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|211338915|gb|FL166533.1|FL166533
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
EST: gi|149101569|gb|EE187695.2|EE187695
EST:     CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAG                         GATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG
genomic: CCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTG

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: 230

CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTGGGCATCACAAGCTCCTTCGGATTTGCTTTTGTTGGTCCAGTTGGGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTGGGCATCACAAGCTCCTTCGGATTTGCTTTTGTTGGTCCAGTTGGGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTGGGCATCACAAGCTCCTTCGGATTTGCTTTTGTTGGTCCAGTTGGGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgc ... ccttttacagGATAAAGATAATAAAGACAATAAAGAGTTTAAAGTTGATTGGAAGAGGGTGGGCATCACAAGCTCCTTCGGATTTGCTTTTGTTGGTCCAGTTGGGCATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCCTCTGGGGCCTCGGCGACATCGGCGCCCAGACCGTCACCTACTACTCCGCTAGCCCCGACCGTCGCGGCCACGACAGCAGCCCTCCCGACCCCGAGgtagcgtcgcagcagcagccccaaccggcttttaccgttccctccgtggtccgtgctcgtgatccgtgtattcatccgccggttcctggacctggtagcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catccgcc