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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttggaaatatgaagactggcaccatctttcgaatagttcccttgactattttggttccggtacatcttaggtaatgatgttttgttggttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA

Basic information

species Zea mays
transcript GRMZM5G812144_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G812144_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g08210.1 (Oryza sativa), 3'ss of exon 15
----agttggaaatatgaagactggcaccatctttcgaatagttcccttgactattttggttccggtacatcttaggtaatgatgttttgttggttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA
     ||||||   |  |   ||      || |     ||| | |  ||   |    ||  |||    ||||||    |||||   |  || | || ||||||||| || ||||||||||| |||||||| |||||  |||||||||| ||||||||||| || ||||||||||||| ||||||||||||  |||| |||||||
cttctgttggattgagtatttctcttcatatatgcaatatattacagtttctttccctgactcc----catctttctcaatgaaactgcgtggttttattacagGAGAACCAGGCACAAAGGCCATGGCCCAAGGACCGGATATGGGTTTTCAAGAGTGACCCAAGATTCTTTGGTACTCCAATGATGGATGCCGTATTGAATA
















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|87156340|gb|DY401129.1|DY401129
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|32939859|gb|CF044678.1|CF044678
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|76285994|gb|DV025562.1|DV025562
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|32932026|gb|CF036838.1|CF036838
EST:     AAGAGCGAGCTTATGGAAGCAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|33094122|gb|CF054116.1|CF054116
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|76285995|gb|DV025563.1|DV025563
EST:     AAGAGCGAGCTTATGGAAACAGACCTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCCAAGGATAGGATATGGGTGTTCCAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|60394723|gb|DN227593.1|DN227593
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|22715732|gb|BU197931.1|BU197931
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|26559581|gb|CA831816.1|CA831816
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAG
EST: gi|211478188|gb|FL010628.1|FL010628
EST:     AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATG                         GAAAAGCAGGCACAAAGACCATGGCCAAAGGA
genomic: AAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGA

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: 180

GTCGTTGCCAGATGTCTCATCCTTCTATGTGAAGTCTGCAAAACCATCACAAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

GTCGTTGCCAGATGTCTCATCCTTCTATGTGAAGTCTGCAAAACCATCACAAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GTCGTTGCCAGATGTCTCATCCTTCTATGTGAAGTCTGCAAAACCATCACAAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 159

GTCGTTGCCAGATGTCTCATCCTTCTATGTGAAGTCTGCAAAACCATCACAAGAGCGAGCTTATGGAAACAGAACTGTGAGATTCATGTTATCGCGCATGgtaagtgcta ... ttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactattttggttccggtacatcttaggtaatgatgttttgttggttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA
                            taatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttggaaatatgaagactggcaccatctttcgaatagttcccttgactattttggttccggtacatcttaggtaatgatgttttgttggttgattacagGAAAAGCAGGCACAAAGACCATGGCCAAAGGATAGGATATGGGTGTTCAAGAGTGATCCGAGATTCTTTGGTAGTCCAATGATGGACACCGTGTTGAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - -caccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt