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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcagtcattttcttctaaaggcaactttacagtttcttacaagcagtaatgtatatacatacaaccatacaagttcagccttgacaattctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA

Basic information

species Zea mays
transcript GRMZM2G012942_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 3
tttgcagtcattttcttc-taaaggcaactttacagtttcttacaagcagtaatgtatatacatacaaccat-acaagttc---agccttgacaat-tctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA
  |   || |||||| |  | | || | | | |     ||    ||||     | ||| ||  |       |   | |||    |   |||    | | |||| ||||||||||||| |||||||  | ||||||||||||||  | |||||||| || ||||| || ||||| || | ||||||
-gtaaggttattttcataatgatgggagcctca-----tccattaagcctccttttatttaggtttttttgttgtatgttgtgaaattttgctgctctttttgtagTGGTTGAAGACATATACAAGAGAAGGCAGCCATTGCCCACCATGGATGCTATATATTTCATCCAGCCAACCAGAGAAAA

upper sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 3
-------tttgcagtcattttcttctaaaggcaactttacagtttcttacaagcagtaatgtatatacatacaaccatacaagttcagccttgacaattctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA
       | ||      |||| || | ||   |  | |||  ||| |  |         | | | | |  |       |    |  |   |  |    ||| ||||||||| |||||  ||||||| || |||||||||||||| |||||||| ||||| || || || ||||| || ||||| ||
gtgtgtgtgtgtgtgtgttttttttttaatatatatataccttttttcgctt-------tttcttttctcatctttgaatgtatcaaatttctatttctctgtgcagTGGTGGAAGATATATACAAGCGAAGGCAGCCATTGCCCTCAATGGACGCAATATACTTCATACAGCCAACCAAAGAGAA
















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|78119731|gb|DV538115.1|DV538115
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
EST: gi|211425195|gb|FL233969.1|FL233969
EST:     ATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGGTTTCAT                         TGGTTGAAGACCTATACAAACGGAGGCAGCCCAT-GCCTTCAAGGGATGCA
genomic: ATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGG-TTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCC-ATTGCCTTCAATGGATGCA
EST: gi|101399517|gb|EB821626.1|EB821626
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
EST: gi|211425196|gb|FL233970.1|FL233970
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTTGAAGACCTATAC
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATAC
EST: gi|211425194|gb|FL233968.1|FL233968
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
EST: gi|211425197|gb|FL233971.1|FL233971
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTTGAAGACCTATACAAACGGAGGCAG
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAG
EST: gi|18170862|gb|BM340702.1|BM340702
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTT-AAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
EST: gi|18163515|gb|BM333354.1|BM333354
EST:     AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT                         TGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA
genomic: AATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAA

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), 46 (downstream exon)
Score: 56

GTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 45

GTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

GTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

GTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCATgtaagtggct ... ttctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtaatgtatatacatacaaccatacaagttcagccttgacaattctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA
                                    ccttgac  putative branch site (score: 78)
                                             ttctttgc  putative PPT
     aatgtatatacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcagtcattttcttctaaaggcaactttacagtttcttacaagcagtaatgtatatacatacaaccatacaagttcagccttgacaattctttgcagTGGTTGAAGACCTATACAAACGGAGGCAGCCATTGCCTTCAATGGATGCAATTTATTTTATGCAGCCTACTAAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- tgcagtc
- - - - - - - - - - - - - - - - - - - - -acaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacaa