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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttcctttgtttcaactttcaaaaacagaataattcatcagcattccttgaatctttcatgtttcatcaatattgatattctttcttaaactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC

Basic information

species Zea mays
transcript GRMZM2G065494_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 3'ss of exon 12
tatttcctttgtttcaactttcaaaaacagaataattcatcagcattccttgaatcttt----catgtttcatcaatattgatattctttcttaaactattc-agCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
     | || | |  ||  ||   | |  || || |  | || | |||| ||   || |     ||||||||| |||||||| |  | || || |||| ||| |||| |||||||||||||||||||||||||| |||||||||||||| ||
----ccattggctgtaatatttttatattgacta-tggaacatccttccatgcgactgttgactatgtttcatgaatattgacacgcgttattgaacttttccagCTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC

upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 3'ss of exon 14
tatttcctttgtttcaactttcaaaaacagaataattcatcagcattccttgaatctttcatgtttca--tcaa--tattgatattctttcttaaactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
   ||    || |   | |  |    |||   ||| |   |||  |   || | | | |   |  |||  ||||  ||||  |  | ||| ||      ||||| | |||||||||||||| || |||||||| ||||| |||||||| ||
---ttgtggtgctatcaatgccctccacatcttaaattg-cagtttattttaattgtgttgggaatcaattcaaactatttgttctttttgttctttctttcagTTAATCAATCCTGCTGAAACTTTTGGGGACATTGTCATTGATTATCC

upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------tatttcctttgtttcaactttcaaaaacagaa-taattcatcagcattccttgaatctttcatgt--ttcatcaatattgatattctttcttaaactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
                                                         ||      ||   |||   |  | |  |||   |     | ||  ||| |   ||   |  |||   ||  |   |     | |   |  ||  | | | ||| | ||||| ||||||||||| ||||| |||||||| ||||||||| |
gtgactttatcgatgccctattgatttcgctgctattctattgcgcaattcgtgatgtaagcttgtttaatcactctctagatgcaggcctcgaagagcataatttccacaacaataaatgaaattatttcttgcccgtttggctgttttgattttccagGTCATCAACCCTGCTGAGACTTTTGGAGATATTGTAATTGATTACTC

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|32943399|gb|CF048218.1|CF048218
EST:     TGGTGGTTTTGCGACTTATGA-CNTCACAAGATCCTATGCCTGGCTGGAG                         CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
genomic: TGGTGGTTTTGCGACTTATGAAC-TCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
EST: gi|22489164|gb|BU049087.1|BU049087
EST:     ATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAG                         CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
genomic: ATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
EST: gi|18383894|gb|BM417094.1|BM417094
EST:     ATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAG                         CTGATCAATCCTGCTGAGACCTTTGGGGATATTGNGATTGATTACCC
genomic: ATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC

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: 48 (upstream exon), 49 (downstream exon)
Score: 236

AATGATAATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 173

AATGATAATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 177

AATGATAATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 265

AATGATAATGGTGGTTTTGCGACTTATGAACTCACAAGATCCTATGCCTGGCTGGAGgtaggtggat ... aactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttgaatctttcatgtttcatcaatattgatattctttcttaaactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC
                           tattgat  putative branch site (score: 265)
                         aatattgatattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttcctttgtttcaactttcaaaaacagaataattcatcagcattccttgaatctttcatgtttcatcaatattgatattctttcttaaactattcagCTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC

- - - - -tgtttca
- - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - -catcagc
- - - - - - - - - - - - - - - - - - - - - - - - cttgaat