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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcctgattctccttccatcttagatgatttaactaatcttgtaataagcataatttttgtttgatgatgcattggtatttcgtaaaatttgctacag

Basic information

species Zea mays
transcript GRMZM2G105772_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105772_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g24200.1 (Oryza sativa), 5'ss of exon 5
------TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcctgattctccttccatcttagatgatttaactaatcttgtaataagcataatttttgtttgatgatgcattggtatttcgtaaaatttgctacag------------------------------
      |||  |||||||||| |   |  ||||||| ||||| ||  |||||||||||||||||||||||| ||||||||||  ||| |||||  || |  |||| | || |||  |  | |   || ||| || |||| ||||   || || ||     ||     |                                  
TGTACCTGTCACTGTCAGTGCTCCTACCCCAACTGCCACAGCTTCCCCAGCTCCTGCTGTTGCTGTATCgtgagttcctgatgttccatccattctata-aatttgattattctcatg-tgaatgtagtttctgcttgaggatgtgctg-taatttactgaacccattttgacttgatcttttcttcttgccatttgagcag
















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|109179157|gb|EC379841.1|EC379841
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|148969759|gb|EE020640.2|EE020640
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|149051783|gb|EE155908.2|EE155908
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|60396086|gb|DN228955.1|DN228955
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|148943103|gb|EC888159.2|EC888159
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|9732269|gb|BE511021.1|BE511021
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|78118533|gb|DV536917.1|DV536917
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|148991633|gb|EE033168.2|EE033168
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|91054260|gb|EB164678.1|EB164678
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|211414779|gb|FL112985.1|FL112985
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTKTTGCTGTATC                         CACCGAGGCAGATAGTTAT
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTAT
EST: gi|21843204|gb|BQ703785.1|BQ703785
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGC
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGC
EST: gi|91876143|gb|EB406100.1|EB406100
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|74240960|gb|DT648874.1|DT648874
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|32861117|gb|CF000799.1|CF000799
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|76011555|gb|DT938725.1|DT938725
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|148956696|gb|EC902566.2|EC902566
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|149001065|gb|EE038319.2|EE038319
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|91057192|gb|EB167610.1|EB167610
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|91878897|gb|EB408854.1|EB408854
EST:     GCACTGGCTGCAACTGCTACCGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CCCCGAGGCAGATAGTTATGGTCAGGCTGCCTCCAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
EST: gi|149096952|gb|EE182751.2|EE182751
EST:     GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC                         CACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG
genomic: GCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAG

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), 49 (downstream exon)
Score: 42

TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTCAATCCATTCTTGAAATGGGTGGCGGGATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 30

TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTCAATCCATTCTTGAAATGGGTGGCGGGATA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 32

TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTCAATCCATTCTTGAAATGGGTGGCGGGATA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcct ... tttgctacagCACCGAGGCAGATAGTTATGGTCAGGCTGCCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTCAATCCATTCTTGAAATGGGTGGCGGGATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATCgtaagttcctgattctccttccatcttagatgatttaactaatcttgtaataagcataatttttgtttgatgatgcattggtatttcgtaaaatttgctacag

- - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT