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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtattctaattgtttgtttcccataaataatatgcacatggattgacaggagtgtaggacaaagcatgtggtacaaccttgttatacatgttta...

Basic information

species Zea mays
transcript GRMZM2G131699_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 5'ss of exon 4
ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaa-gtgtattcta-attgtttgtttcccataaataatatgcacatggattgacaggagtgtaggacaaagcatgtggtacaaccttgttatacatgttta-
  |||| | |||  || |||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||||||||  | | | | | | ||||   |  | |  | |   ||||   ||||| || ||||         |||| |    ||          | ||||||   | 
GTTCAAGTGTTATCACGCAACCAGACCGTTATTTGATGATCGTTACAAGTGGAGGCCTCAATCAACAGAGAACAGGGgtaatatatgtgccacactgttccgtatcaaatactgtgatgcgtgtggatggataggaaaaagaataaaagaaatcagtttg---caaatgtacatgaagaa

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G02110.1 (Glycine max), 5'ss of exon 2
--ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtattctaattgtttgtttcccataaataa-tatgcacatgg-attgacaggagtgtaggacaa-agcatgtggtacaaccttgttatacatgttta
   ||||| |   | ||| || ||  | || |||||||||||    |||||||||||| |||||||||| ||||| ||||||| | |  |  |||  |    ||   |||   ||  | | |  ||  | || |    || |     |  |  |  | ||     | ||      || ||  
AAGCTCAAGTG--ATTACACAGCCGAATCGGTATTTGATGATCACAACAAGTGGAGGCTTGAATCAACAAAGAACTGGGgtaattct-ctggaatattgatattattatagtcaaacaaggatttgatactgccttctgtttctactactaaaaaattgtgttttcctgagtctgatttt--

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G02010.1 (Glycine max), 5'ss of exon 4
--ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtattctaattgtttgtttcccataaataa-tatgcacatgg-attgacaggagtgtaggacaa-agcatgtggtacaaccttgttatacatgttta
   ||||| |   | ||| |||||  | || |||||||||||||  |||||||||||| |||||||||| ||||| ||||||| | |  |  | |  |  | ||   |||   ||  | | |  ||    || |    || |     |  |  |  | ||    |   ||   |  | ||  
AAGCTCAAGTG--ATTACACAACCGAATCGGTATTTGATGATTGCAACAAGTGGAGGCTTGAATCAACAAAGAACTGGGgtaattct-ctagactcttgagattattatagtcaaacaaggatttgatgctgccttccgtttctactagtaaaaaattgtgtttctgagtctgatttttt--

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv03s0038g03240.t01 (Vitis vinifera), 5'ss of exon 4
ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtattctaattgttt-----gtttcccataaataatatgcacatggattgacaggagtgtaggacaaagcatgtggtacaaccttgttatacatgttta
|      | | |  || ||||   |  | || ||| |||||| ||| ||||||||| | |||||||| ||||||||||||| | | ||  ||||  ||     ||||    |  ||||  | |   |  ||| |    | |      ||||         |      ||||  | | |    
AAGTTGGTGTCAGCACACAACGGAATAGATACTTGTTGATTGCTACCAGTGGAGGCTTAAATCAACAAAGAACAGGGgtaactttctttcaattaattaacaagttttttgtttataa-gttcctgtttattaattaaaataatattcaaaattaaattgatgtttctgttgaatacg----

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 5'ss of exon 4
ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagt------gtattctaattgtttgtttcccataaataatatgcacatggattgacaggagtgtaggacaaagcatgtggtacaaccttgttatacatgttta
|  |      ||  ||    ||  | || |  |||||||||| ||| ||||||||| | |||||||||||||| ||||||| |      | ||||  ||| | | ||    | || | ||         |||    |    | |   | |||  |      | || | |||| || |||    
AAGCTGTAGCTATCACAGTTCCCAATCGATTCTTGATGATTGCTACCAGTGGAGGCTTAAATCAACAGAGAACTGGGgtaattcttgtagcattcatattatatattagttaaaatttatccaagttcagatccttac--ctatcaaaaaaaaaagaaaaaagaagcatgtt-tatatgc---

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|76010763|gb|DT937933.1|DT937933
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
EST: gi|89249642|gb|DY621428.1|DY621428
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
EST: gi|149110252|gb|EE190310.2|EE190310
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
EST: gi|31909461|gb|CD650930.1|CD650930
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAAT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAAT
EST: gi|78111344|gb|DV529741.1|DV529741
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCCCACTTGTTGTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
EST: gi|71322750|gb|DR798057.1|DR798057
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
EST: gi|211056621|gb|FL260439.1|FL260439
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGT                         ATAATCGAATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGA-TGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTT
EST: gi|71308473|gb|DR790475.1|DR790475
EST:     GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG                         ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT
genomic: GCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTT

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: 45 (upstream exon), 46 (downstream exon)
Score: 52

ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 25

ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 36

ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG


Block sizes: 45 (upstream exon), 37 (downstream exon)
Score: 24

ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtat ... gctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGGgtaagtgtattctaattgtttgtttcccataaataatatgcacatggattgacaggagtgtaggacaaagcatgtggtacaaccttgttatacatgttta

- - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG