Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattcttgcag

Basic information

species Zea mays
transcript GRMZM2G152827_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 4
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatctacgtcttgtaccta--ctagctattggttatatattgttgctatattcttgcag---------
||||||||||||||| || ||||||||||| ||||| ||||| || ||||||||| | || |||||| ||||||| |||||||||||||||||||| ||||||||||| | ||||  || ||  | |  |  | | |  | || || |  ||   || | | ||  ||  || ||| |    |     || |          
TGGTGGTTACATTGCTGGAGTCTTCTGTGCCATTGTCTCTCATCCAGCTGACAACTTGGTCTCTTTCTTGAACAACGCCAAGGGAGCTACAGTGGGTGATgtaagcatgtcttct-actaataaaacccat-tatgtgcaagttttatttcttatcttgatgttactttcatgttggttgactgcatatgaaagttgcattt

upper sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 5
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgct-catgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag
|||||| || ||||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |  || |||| | ||||  |   | |  | | | | | ||| | ||  |    |   | |   |    ||  |||| | |    |||||
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgt-catacttggtgcatgtttagtataattgttt-catattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag

upper sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 4
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag
|||||| ||  |||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |      | |  ||||  | |      |   |  || ||  | ||  |    |   |||   |    ||  |||| | |    |||||
TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgcatgt-ttagtgtcattgttttgtattacatctgtttttgacgagtttctttgattttatatactatataatgcag

upper sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G05460.1 (Glycine max), 5'ss of exon 4
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag
|| |||  | ||||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |      | |  ||||  |   | |  | | | | | ||| | ||  |    |   | |   |    ||  |||| | |    |||||
TGCTGGAAATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtcagacttggtgcatgtttagtataattgttt-catattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag

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|32849572|gb|CD989253.1|CD989253
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAGGGGAGCTACAGTGGGAGAT                         GCTGGTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTA
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTA
EST: gi|32848897|gb|CD988578.1|CD988578
EST:     ACAACCTTGTGTCCCTCCTGAACAATGCCAAGGGAGCTCCAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|32849561|gb|CD989242.1|CD989242
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAGGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGATCTTC-TCT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGA-CTTCCTCT
EST: gi|166611021|gb|EG296956.1|EG296956
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCAC
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCAC
EST: gi|31612075|gb|CD568697.1|CD568697
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCCCTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|26456075|gb|CA827658.1|CA827658
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|32849444|gb|CD989125.1|CD989125
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAGGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|32927274|gb|CF032086.1|CF032086
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|33102415|gb|CF062375.1|CF062375
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|211458338|gb|FL363660.1|FL363660
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|5928934|gb|AW056226.1|AW056226
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGNTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|71433232|gb|DR814282.1|DR814282
EST:     ACAACCTTGTGTCTTTCCTGAACTATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|149100649|gb|EE186737.2|EE186737
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|116817564|gb|EC860439.1|EC860439
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|161591368|gb|EY962203.1|EY962203
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGG
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGG
EST: gi|113680402|gb|DW838476.1|DW838476
EST:     AACCTTAGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGTAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTT
genomic: AACCTT-GTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAG-ATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTT
EST: gi|166543385|gb|EG150338.1|EG150338
EST:     CTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTACT
genomic: CTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCT-CT
EST: gi|110965377|gb|EE185277.1|EE185277
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|31358410|gb|CD442767.1|CD442767
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|32849863|gb|CD989544.1|CD989544
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTGCAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|15080205|gb|BI388980.1|BI388980
EST:     ACACCCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|32927695|gb|CF032507.1|CF032507
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|67021830|gb|CO450579.1|CO450579
EST:     ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
EST: gi|32945563|gb|CF050382.1|CF050382
EST:     ACAACCTTATGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGAT                         GCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT
genomic: ACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 1161

TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 1636

TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1204

TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 1490

TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatat ... attcttgcagGCTGTTAAGAAGCTTGGTCTCTGGGGTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT