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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacagaaattttaaatacctggaaactgttcaagatattaatcgcttctcgatattttctcgaagacgagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 8
gaacagaaattttaaatacctggaaactgttcaagatattaatcgcttctcgatattttctcgaagac--gagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
 ||     | ||    || ||| ||||  |||||  || ||   ||   |  ||  ||  |  || |    || || |    ||  |  || |||||||||| |||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||
aaaagcttaattgggctatctgaaaac-attcaac-tactatgtgcaattaaatccttattgaaaaatcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG

upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 7
---gaacagaaattttaaatacctggaaactgttcaagatattaatcgcttc--tcgatattttctcgaagacgagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
     |  |   |||   ||     |||  ||||    ||||| | |  ||   || | ||| | | ||  | ||    |||  |||   || |||||||   |||| |||||||||||||| || || ||||| ||||| ||||||||||||||||| |||||||||
aaaagattgctgtttgctatttgcagaacttgttgtgcatatttagcattttaatcaagattctattgac-atgacatttgatgttt---tgcttttctgc-cagACCTTCATTGACAAGTTCCGTTATAATGCGAAGAGGGCATCACTTGTTCAATCTAGAATCAAG

upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 7
---gaacagaaattttaaatacctggaaactgt-tcaagatattaatcgcttctcgatattttctcgaagacgagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
     |  |   |||  |||     |||  |||  |    ||  | |    ||  |||  | | |   | | ||    |||  |||   || |||||| |  |||| |||||||||||||| || || ||||| ||||| ||||||||||||||||| |||||||||
aaaagattgctgtttgcaatttgcagaacttgtgcctctgtagcattttaatcaagattctatttgacatatgacttttgatgttt---tgcttttctat-cagACCTTCATTGACAAGTTCCGTTATAATGCGAAGAGGGCATCACTTGTTCAATCTAGAATCAAG

upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------gaacagaaattttaaatacc---tggaaactgttcaagatat---taatcgcttctcgatattttctcgaagacgagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
                    ||  ||| |  ||||| |    |  ||   ||    | | |   ||||    |  | | ||    |  |||      | |  |  |   |||||||    |  || | |||||||| || ||||| |||||||||||||| || || |||||||| ||||||||||||
gtttcttttcttcttctggaaaatgaactcataaattctgtttccaactcgtctctggtttgtttaataatattccaacatgggatgtaagtttgatgcttgatatc--ttgttttctgctacagGCGTTCATTGATAAATTTCGTTACAATGCAAAGAGGGCGTCTCTTGTTCAGTCAAGAATCAAG

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|33094472|gb|CF054466.1|CF054466
EST:     ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAG                         ACATTCATTGACAAGTTTCGGT
genomic: ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGT
EST: gi|60343993|gb|DN210966.1|DN210966
EST:     ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAG                         ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|211238345|gb|FL044423.1|FL044423
EST:     ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAG                         ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|211429008|gb|FL174617.1|FL174617
EST:     AGCACATGCAG                         ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: AGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAG                         ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAG                         ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAA

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), 47 (downstream exon)
Score: 233

CAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 187

CAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 201

CAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 172

CAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATCAGCAGAAAGCCTTTGAAACAAATGAGAAGGCCAGACAGCACATGCAGgttggttgta ... ttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcgatattttctcgaagacgagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
                                 ctttcattgtttttct  CT-rich tract
       atattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacagaaattttaaatacctggaaactgttcaagatattaatcgcttctcgatattttctcgaagacgagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
-aacagaa
- - - - - - - - -acctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatt