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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttagcagctacatattttaagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG

Basic information

species Zea mays
transcript GRMZM2G044011_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------------------------------tggttagcagctacatattttaagactttaatt---tatatttttaa----ctgaagaacacatattgcta--tatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
                                                                                            |  ||  | ||  ||| |       ||| |||   |||  ||||||     |||   ||   |   | |   | ||  || | |  |    |||  || ||||||||||||||||| |||| | ||||||||||||||||| |||||| |||||||||||||||| |||||||| || ||| ||
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagc-tatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
tggttagcagctacatatttt----aagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
|||||     ||     |       || |||  || ||| ||   | |      |    |||||   ||  |  || | |  |  ||| | ||     ||| || || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  
tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaat----aaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G36200.1 (Glycine max), 3'ss of exon 7
--tggttagcagctacatattttaagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
  |   ||   | |     | || | | | || || |  |||   |   ||        ||||| ||  |  ||   |       |||   |    |||||| || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  
attaaatacatgttcttcttgttgatagtctagttaacttttggcatgtaattgtgt-cattgcaatg-aattgatttgtcttattatgtctaataaaacagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------tggttagcagctacatattttaagactttaatttatat--ttttaactgaagaa-cacatattgctatatagatgg-catcctgatgtatcattttcta----------------aacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
                                                        || || |     |  || ||      ||| |  |   |  ||||  ||||| ||  |   |  |    | |||    |||||   | | |  || | ||                  |||  | |||   | ||| ||||| || |||||||| ||||||||||||||||| |||||||||||||| |||||| | 
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT

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|19351008|gb|BM895540.1|BM895540
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19272449|gb|BM888705.1|BM888705
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATA-CAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19351610|gb|BM896142.1|BM896142
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19351009|gb|BM895541.1|BM895541
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCGCCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|22491504|gb|BU051427.1|BU051427
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGGCAT
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAA-CCCGGGCACGTATTGAAACATCAATTCCTAGGAAG-CAT

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), 49 (downstream exon)
Score: 53

ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 123

ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 75

ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
                              tcctgat  putative branch site (score: 75)
                                        tcattttct  putative PPT
                                      tatcattttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttagcagctacatattttaagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG

- - - gcagcta
- - - - - - - - - - - - - - - - - - - - - - - -aagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tattgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatg