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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagtattgagcactgagcgcgtgtccttgttttttggcggtgaagagaaattgatcacaagtatgtaacagcacttaatgatggatggatggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT

Basic information

species Zea mays
transcript GRMZM2G051842_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------------------------tcaagtattgagcactga-gcgcgtgtccttgttttttggcggtgaagagaaattgatcacaagtatgtaacagcacttaatgatggatggatggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT
                                                                                       | | | || |  ||  |  | |  ||   |  |||   |   ||      ||   ||   |   | ||| |        | |||   ||  |   |||||||| ||||||||| |||| | ||||||||| || ||||||||| | || || ||||| || ||||| ||||||||||||||||||||| ||||||| ||| 
gtgagatcaaggttattgtgatgtactacaatagcaatgttatttgggatgttattgtgatgcatactagtatttgatacacatgcatgatgcatggttcagagttgagaatggtttcctttgcagtttgtttgagcaacaagaaggcggctttgttaacatgtaaagtgaaaaataaa---atgcagGTGGTTCAAGTGGCGGCAACCGGGGAGAGTAATGCGGTGGACGCGACGGGGGCGGGGGATCTGTTTGCGAGCGGGTTCCTGTACGGGTTGGTGAAAGGGC
















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|29576892|gb|CB617004.1|CB617004
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|149079176|gb|EE168123.2|EE168123
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|18179998|gb|BM381208.1|BM381208
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|29543849|gb|CB604229.1|CB604229
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|211429772|gb|FL436587.1|FL436587
EST:     CTGTGGTCACASTTGCTTCAAAGGGATGCATGGCAAMGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|31612067|gb|CD568689.1|CD568689
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|29945521|gb|CB815681.1|CB815681
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|29945789|gb|CB815820.1|CB815820
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|31911174|gb|CD651792.1|CD651792
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|148928772|gb|EC873535.2|EC873535
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|71762333|gb|DR960270.1|DR960270
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|78103938|gb|DV522356.1|DV522356
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|28873361|gb|CB329360.1|CB329360
EST:     TTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: TTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|211123067|gb|FL031406.1|FL031406
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|29543893|gb|CB604273.1|CB604273
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|71771408|gb|DR969345.1|DR969345
EST:     TGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: TGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|78105422|gb|DV523840.1|DV523840
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|60338856|gb|DN205829.1|DN205829
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|101385265|gb|EB814678.1|EB814678
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
EST: gi|30032244|gb|CB834095.1|CB834095
EST:     CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAG                         GTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA
genomic: CTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGA

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: 137

ATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 34

ATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

ATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

ATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAGCATGGCAAACAGgtgagtttta ... atggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaaattgatcacaagtatgtaacagcacttaatgatggatggatggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT
                               ttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagtattgagcactgagcgcgtgtccttgttttttggcggtgaagagaaattgatcacaagtatgtaacagcacttaatgatggatggatggatgcagGTCGTTCAAGTGCCGGCCATCGGGGAGAGCAACGCGGTGGACACAACTGGAGCGGGCGACCTGTTCGCGAGCGGGTTCCTGTACGGGCTGGTGAAGGGGT

- - - - - -gcactga
- - - - - - - - - - - - gtccttg
- - - - - - - - - - - - - - - - - - - - - - aagagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggatg