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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactgttttcttcacattattcatgtattcttatggcagtttgcataccacatgatacatttttctatgctgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 10
--tgactgttttcttcacattattcatgtattcttatggca-gttt--gcataccacatgatacatttttcta-tgctgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG
    |    | | ||||| |  | ||| | ||  |||| || || |  ||  | |      |  |||||  |  |||| |||||||     | |  ||||| ||||||||||||||||||| |||||||||||||| |||||||||||||||||||| ||||| || || || || |||||
ttgaaaaaatatattcac-tagtacatttgtttctatgacacgtctcagctaaacgtcaactgtattttcttggtgctaatgttgc-----tgtgcttttgctcagTGTTCTTGTTCATAGCGGAGGAGTACATGGCGGTCACTACTATGCTTTCATACGGCCTACGCTATCAGACCAGTG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 10
----tgactgttttcttcacattattcatgtattcttatggcagtttgcataccacatgatacatttttctatgctgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG
    |   | |||| |       |  |||| |    | |  || ||    |      || || ||||  | |   |||  |  |  | | || ||| | | ||||||| | |||||||||||||||||||||||||| ||||| |||||||| ||  |||| || ||||| ||||||||
ttaattggtattttatgagtggaagacatgaaaatgt-tatcatttcatttggtgtctgttatattt--ccagcttgacat-actagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------tgactgttttcttcacattattcatgtattcttatg--gcagtttgcataccacatgatacatttttctatgc---------tgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG
                                                 |     |    ||    ||||| || |||| || |    |||   |  | ||   ||  | | |||  |             |||| ||| || |||||| ||     |||||| || ||||| ||||| ||||||||||||||||| ||||| ||||| ||  | || |||||||| || |||||
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG

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|5439328|gb|AI820249.1|AI820249
EST:     CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAG                         TGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
genomic: CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
EST: gi|5740126|gb|AI947816.1|AI947816
EST:     CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAG                         TGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
genomic: CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
EST: gi|101389686|gb|EB816777.1|EB816777
EST:     CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAG                         TGTTCTTGTTCATAGTGGAG
genomic: CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAG
EST: gi|78026582|gb|DV494969.1|DV494969
EST:     CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAG                         TGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
genomic: CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
EST: gi|5398807|gb|AI812151.1|AI812151
EST:     CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAG                         TGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT
genomic: CTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCAT

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: 47 (upstream exon), 48 (downstream exon)
Score: 224

GCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 189

GCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 165

GCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 151

GCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATACTCTTCACAGgtaatttatt ... ttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccacatgatacatttttctatgctgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG
                       tgctgat  putative branch site (score: 151)
                               ttgcctgttttttttt  CT-rich tract
                                    tgtttttttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactgttttcttcacattattcatgtattcttatggcagtttgcataccacatgatacatttttctatgctgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- actgttt
- - - - - cttcaca
- - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - -cacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tacattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg