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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcattcatactatctatcagttatggagtttttttagcagaacttgtcagttatattgttatctgagtaaaactgatcttaactgctaaggtgtgcaatctgtattag

Basic information

species Zea mays
transcript GRMZM2G104166_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104166_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g45670.1 (Oryza sativa), 5'ss of exon 3
-----------GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcattcatactatctatcag-ttat-ggagtttttttagcagaacttgtcagttatattgttatctgagtaaaactg-atcttaactgctaaggtgtgcaatctgtattag
           ||||||||| ||||| |||||||| || |||||||| |||||||||||||| || |||||||  |   ||  ||||| ||| || ||||  || |  |||||||   ||     | | ||       | |    |  |||| || || | |  |         ||| | ||    
CATTTTCAAAGGGACATTGTCCGGGGTGTGGAGGGATACATAGTCACTGGATCTAAACAAGTTGACATAGgtatgtttctccaactatatattagcttatcagaataattttagcttgacacaatattaattactcagtgtttacattactgtatgttgattagttgcaacctaaatttatag---
















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|91056507|gb|EB166925.1|EB166925
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|74236878|gb|DT644792.1|DT644792
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|50336720|gb|CO531846.1|CO531846
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|148996413|gb|EE035708.2|EE035708
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|20301506|gb|BQ164449.1|BQ164449
EST:     TCGGGGCGTGGAGGGCTATATAGTCTCAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|33466753|gb|CF243802.1|CF243802
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|76283090|gb|DV022658.1|DV022658
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|91873694|gb|EB403651.1|EB403651
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|148981761|gb|EE027867.2|EE027867
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|26456480|gb|CA828063.1|CA828063
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|148970807|gb|EE021570.2|EE021570
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|76927135|gb|DV171161.1|DV171161
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
EST: gi|93012221|gb|EB637741.1|EB637741
EST:     TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG                         GGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA
genomic: TCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTA

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), 40 (downstream exon)
Score: 91

GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTACAAGTGGTGATACTTTGTCCAAAGCTGCTACATATTTCGGAAAGGCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTACAAGTGGTGATACTTTGTCCAAAGCTGCTACATATTTCGGAAAGGCACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 246

GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTACAAGTGGTGATACTTTGTCCAAAGCTGCTACATATTTCGGAAAGGCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 348

GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcatt ... tctgtattagGGAATAAATTGTCTGATGACAGCCAGAAATACGGTGTTGGAAACACATGTACAAGTGGTGATACTTTGTCCAAAGCTGCTACATATTTCGGAAAGGCACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAGgtagttcattcatactatctatcagttatggagtttttttagcagaacttgtcagttatattgttatctgagtaaaactgatcttaactgctaaggtgtgcaatctgtattag

- - - - - - - - GTGGAG
- - - - - - - -  TGGAGG