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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatattattagtgttttggttgaaaatttctttcaaaaagaaaaaatgaatcaggagaaaagtttacattgagaaaattgagaaccatcaacgactttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g52500.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G007157_T02 (Zea mays), 5'ss of exon 9
GGCAACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatattattagtgttttggttgaaaatttctttcaaaaagaaaaaatgaa--tcaggagaaaagtttacattgagaaaattgagaaccatcaacgactttgcag
|| || ||| ||| ||||||||| || |||||||| || | ||||||||||||||| |||||| ||| | |||||  ||  |  |  | ||     |    ||   ||  || | ||| |||   |  |   | ||||       | |   |   || ||||
GGAAAATACGTCTATGTTGATGGCGACGGATCTGTTCCCGCAGAATCAGCAAAGgtctgatatcattggcgttttacttttat-taccatttgggcatttgaagcaaagctctgtagagaag---aagtcagggaaat--gttttccttctccttttcgcag
















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|29627576|gb|CB632587.1|CB632587
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|27576266|gb|CA998960.1|CA998960
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|218500790|gb|FG960830.1|FG960830
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29614249|gb|CB619262.1|CB619262
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29627613|gb|CB632624.1|CB632624
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|86493449|gb|CI136082.1|CI136082
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|33799965|gb|CF325850.1|CF325850
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29614251|gb|CB619264.1|CB619264
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|86500894|gb|CI143527.1|CI143527
EST:     GATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: GATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29645191|gb|CB650198.1|CB650198
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29629570|gb|CB634579.1|CB634579
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTGGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|218497772|gb|FG957253.1|FG957253
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29644324|gb|CB649331.1|CB649331
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29614208|gb|CB619221.1|CB619221
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
EST: gi|29665283|gb|CB661558.1|CB661558
EST:     ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAG                         GCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA
genomic: ACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGA

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 1 RNA-Seqlibrary.


Block sizes: 54 (upstream exon), 74 (downstream exon)
Score: 22

GGCAACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatatt ... gactttgcagGCAGATGGCCTCGATGCAGTGGCAAGAGTTGGGGTTGCTGCAGACCACCGAGGAATCGTCTGTGATCGTCACGTGTTCCGGATAATTCAGCACTGGCTCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAACTACATCTGTGTTGATGGTGATGGATCTGTCCCTGTAGAATCAGCAAAGgtatgatattattagtgttttggttgaaaatttctttcaaaaagaaaaaatgaatcaggagaaaagtttacattgagaaaattgagaaccatcaacgactttgcag

- - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - GCAAAG