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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaaaaatcaccgatacataaaagagcatgagtctatgatgtatgaaatgcacttcaatcaggagaaatgaaaactaattcagtacattctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G110626_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 2
--aagaaaaatcaccgatacat-aaaagagcatgagtctatgatgtatga-aatgcacttcaatcaggagaaatgaaaactaattcagtacattctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG
   |   || | |    || || |     |||  |  | |  ||   ||| ||| |       |  |  | |||||   |||||| || | || || |||  ||||||| ||||| ||||| ||||||||||| || || |||||||| ||||||||  | | |||||||||||| ||||| ||||| ||||||
attaatgaagttagacttagatcagttctgcaccacacca--atccctgataattccaaaaggttggctggaatgag--ctaattgagcatatccttcttgtagATGCTTGTGGATGATATTGGTGATGTTACCATAACAAATGATGGAGCAACCATTTTGAGGATGTTGGAAGTCGAGCATCCAGCAGCCAAG

upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 2
aagaaaaatcaccgataca-taaaagagcatgagtctatgatgtatgaaatgcacttcaatcaggagaaatgaaaactaattcagtacattctgc-ttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG
    |     |    ||   ||||   ||  ||   | |  | | |    |       | |      ||  |      |  | |        ||  || |||||| | ||||| ||||| |||||||| || || || ||||||||||| || || |||| ||||||||| || |||||||| ||||| |||
--ccatttctagttttattctaaatctgctcgatattgtcctttgtattttcgttcctagttcctccaatcgtgtttcatgttatgttggcttgtgtttcagATGTTGGTGGATGATATTGGTGATGTGACTATTACAAATGATGGTGCTACTATTCTTAGGATGTTGGAGGTCGAGCACCCTGCTGCTAAG

upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 2
-----aagaaaaatcaccgatacataaaagagcatgagtctatgatgtatgaaatgcacttcaatcaggagaaatgaaaactaattcagtacattc-tgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG
     |      ||     ||   |   |  |  | |   | ||   |   ||  |   || |  ||            ||| ||   || ||||  || || |||||||| || || ||||| |||||||| ||||| |||||||||||||| || ||||| |||||||||||||||||||| ||||||||||||
ttggcagtgtgcatttttaattggttgcaaggttttaacttctgtgcttgtaagagtgttttatacac------cctgtacttatgttgttcattgatgatttcagATGCTGGTTGATGATATTGGTGATGTAACAATTACTAATGATGGTGCTACAATACTCAAGATGTTGGAAGTTGAGCATCCAGCTGCCAAG

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|211160355|gb|FL101555.1|FL101555
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAAC-
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160352|gb|FL101552.1|FL101552
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160359|gb|FL101559.1|FL101559
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160360|gb|FL101560.1|FL101560
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211158769|gb|FL101548.1|FL101548
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211158771|gb|FL101550.1|FL101550
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAAC-
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|22491073|gb|BU050996.1|BU050996
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160354|gb|FL101554.1|FL101554
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160357|gb|FL101557.1|FL101557
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160358|gb|FL101558.1|FL101558
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160351|gb|FL101551.1|FL101551
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
EST: gi|211160353|gb|FL101553.1|FL101553
EST:     CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG                         ATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC
genomic: CGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACC

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), 49 (downstream exon)
Score: 498

TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 162

TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 95

TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 142

TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAGgtatgcatac ... ctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgcacttcaatcaggagaaatgaaaactaattcagtacattctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG
                            aactaat  putative branch site (score: 142)
                                           ttctgctt  putative PPT
                     aaatgaaaactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaaaaatcaccgatacataaaagagcatgagtctatgatgtatgaaatgcacttcaatcaggagaaatgaaaactaattcagtacattctgcttacagATGCTAGTGGACGATATCGGTGATGTTACAATCACTAATGATGGTGCAACCATACTTAAGATGTTGGAAGTTGAGCACCCAGCTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
aagaaaa
- - - - - - - - acataaa
- - - - - - - - - - - - gagcatg
- - - - - - - - - - - - - - - - - - - -atgtatg
- - - - - - - - - - - - - - - - - - - - - - - -aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa