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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggttggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA

Basic information

species Zea mays
transcript GRMZM5G841900_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 3'ss of exon 1
-----------gtagggtt---ggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA
            |||||||   |  ||||| | |  || |||| |  ||    | ||  | ||| |  ||||||| |    ||| |||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || 
gtagggttcagctagggttttggatttggtggcgcctcggattcctcttctgatggtctgcgtggttggttggttcg---attttggctgcagAGGTCCACGGTGGAGGTGGTCGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATTGCGCGT
















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|211118858|gb|FL110173.1|FL110173
EST:     TCACCGGGCGCCG-CGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|148935198|gb|EC879233.2|EC879233
EST:     GCCGCATCGTGCCGCCCGCACCTGGTTCGGACGACCAG                         AGTTCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: GCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102907|gb|FK962288.1|FK962288
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACA
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGA-GGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCA
EST: gi|148991615|gb|EE033149.2|EE033149
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCNCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118856|gb|FL110171.1|FL110171
EST:     TCACCGGGCGCCGCCGCAYCGTGCCGCCCGCACCTGCCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|60341943|gb|DN208916.1|DN208916
EST:     GCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: GCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102909|gb|FK962290.1|FK962290
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGASGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|28873659|gb|CB329617.1|CB329617
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118857|gb|FL110172.1|FL110172
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|148965500|gb|EE016317.2|EE016317
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102908|gb|FK962289.1|FK962289
EST:     TCACCGGGCGCCGCCGCATCGTGCCGSCCKCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     CACCGGGCGCCGSCGCATCGTGCCGCCMGCACCTGGCTCCGACGAACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACA
genomic: CACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG-ACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCA
EST: gi|71439027|gb|DR820077.1|DR820077
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|148935199|gb|EC879234.2|EC879234
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG

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: 63

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 22

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 12

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA
 ttctgat  putative branch site (score: 12)
                                       ttcgttt  putative PPT
        ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggttggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT