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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgttcaaattacatacatacatttgattcgggaaatcaatgatattctggcagggtactttaagtgcatgaatagctcaaattctgaattactaaatgcag

Basic information

species Zea mays
transcript GRMZM2G169516_T05
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169516_T05 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 5
GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgttcaaattacatac-atacatttgattcgggaaatcaatgatattctggcagggtactttaagtgcatg-aatagctcaaattct-gaattactaaatgcag
||||||||| || | ||||| |||||||||||||||||||| |||||       |    | | ||    ||| |    ||   | | |||| || ||||  |  | ||  ||  | || ||| ||  |||||   ||| ||||| ||||||||||
GGAAGTTTTGACTATTTGGATGCTATACGCAATGCTGGAGTACAGgtctgtaaatttgctcatatgttgtacttccacttacagcagtcaaggaaattc-agttgtgtggttcgaatgtatggaaaggctcattctcttgaatttctaaatgcag
















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|71430054|gb|DR811104.1|DR811104
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|15312691|gb|BI478322.1|BI478322
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|148972168|gb|EE023038.2|EE023038
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|71438048|gb|DR819098.1|DR819098
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|32928612|gb|CF033424.1|CF033424
EST:     TTCAGGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: TTCAGGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|149026795|gb|EE046156.2|EE046156
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATT
EST: gi|24934455|gb|CA452673.1|CA452673
EST:     TTCAGGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: TTCAGGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|71442934|gb|DR823984.1|DR823984
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAAGAGT-CATTATTGATGCTTTGCAACTTTACTA
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAA-GAGTTCATTATTGATGCTTGGCAACTTTACTA
EST: gi|71324172|gb|DR798789.1|DR798789
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTTAT-GATGCTTGGCAACTTTACTA
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATT-ATTGATGCTTGGCAACTTTACTA
EST: gi|71318677|gb|DR796095.1|DR796095
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|24765189|gb|CA400348.1|CA400348
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|71433348|gb|DR814398.1|DR814398
EST:     GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCTAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|6973599|gb|AW438335.1|AW438335
EST:     CGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: CGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
EST: gi|71431465|gb|DR812515.1|DR812515
EST:     GGAAGTTTTTACAAC-TGGAGGGCTATACGCAATGCTGGAGTCCAG                         TGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT
genomic: GGAAGTTTTTACAACTTGGA-GGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTAT

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), 45 (downstream exon)
Score: 67

GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTATGCACGGTCCAAGGGTGCAGATGCTGTTCTTCTAATAGCTGCTGTATTAC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 168

GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTATGCACGGTCCAAGGGTGCAGATGCTGTTCTTCTAATAGCTGCTGTATTAC


Block sizes: 44 (upstream exon), 41 (downstream exon)
Score: 34

GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTATGCACGGTCCAAGGGTGCAGATGCTGTTCTTCTAATAGCTGCTGTATTAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 101

GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgtt ... ctaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTATGCACGGTCCAAGGGTGCAGATGCTGTTCTTCTAATAGCTGCTGTATTAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGgtgccatgttcaaattacatacatacatttgattcgggaaatcaatgatattctggcagggtactttaagtgcatgaatagctcaaattctgaattactaaatgcag

- - - - - - -  TTGGAG
- - - - - - - - TGGAGG
- - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - -  GCTGGA