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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcggattcaagtctgttttgctaagcaagattgaaccattcaactgcttcattgttgattctattggttataaccaatctgtcttttttgggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA

Basic information

species Zea mays
transcript GRMZM2G152888_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 2
--gtcggattcaagtctgttttgctaagcaagattgaaccattcaactgcttcattgttgattctattggttat-aaccaatctgtcttttttgggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA
   |        | |||||| || |  ||||| ||    | ||||| |  |||| |||| |||  ||||| ||| ||||||||  | ||| | || || |||||||||||| |||||||| || |||||||| |||||| | ||||||||||||||||||||   ||| || |||| |||||||||| || |
ggattttgcatgactctgttatgtt--gcaaggttatctccttcaattatttcagtgttaattgcattggatattaaccaatccatatttat-ggtttcacagGATTGCTTCGGTAGGCCCATAGCAAGTGCACCAGATGCTTGGTTTGATGTTGTTGAGCGCTACTCCAATGACAGTAACAAGACATTAAA
















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|211452250|gb|FK947270.1|FK947270
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
EST: gi|211452245|gb|FK947265.1|FK947265
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
EST: gi|211452253|gb|FK947273.1|FK947273
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTTGCTT-GGTAGGCCGATCGCA-GTGCGCCCAGAT-CATGGTTTGATG
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATT-GCTTTGGTAGGCCGATCGCAAGTGCGCC-AGATTCATGGTTTGATG
EST: gi|211527655|gb|FL070682.1|FL070682
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
EST: gi|211452252|gb|FK947272.1|FK947272
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGNTTTGATGT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGG-TTTGATGT
EST: gi|76014233|gb|DT941403.1|DT941403
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
EST: gi|211452244|gb|FK947264.1|FK947264
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
EST: gi|211452248|gb|FK947268.1|FK947268
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
EST: gi|78083290|gb|DV511683.1|DV511683
EST:     GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAG                         GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT
genomic: GCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTT

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), 40 (downstream exon)
Score: 130

GGGTACGCGCCGATCTGCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

GGGTACGCGCCGATCTGCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

GGGTACGCGCCGATCTGCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 168

GGGTACGCGCCGATCTGCCTGGGCCTGGAGGATTTCTATGTGCGACGCCTGTACTTGCGGATCCAGgtgagataag ... gggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcattgttgattctattggttataaccaatctgtcttttttgggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA
                       ttataac  putative branch site (score: 168)
                                     tcttttttg  putative PPT
             attctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggattcaagtctgttttgctaagcaagattgaaccattcaactgcttcattgttgattctattggttataaccaatctgtcttttttgggtttacagGATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA

- - - - - - - - ttttgct
- - - - - - - - - - - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat