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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgttacaaaaatcttgaaaacccctgctttacaattgagatgcattatacttttcatagccagtctacaaattctacctggtttatctgatccatgttggtagttgggtccttttattaattgatttgaacatggaagaagtgtgcataattgttttaccattgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCTGAGCTGATGAGCTTTTTCTCAAAGTATCACGATTAAACCACAACAAGAT

Basic information

species Oryza sativa
transcript LOC_Os01g62410.2
intron # 7
splice site 3'
intron type U2

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|58587466|gb|CF985774.1|CF985774
EST:     ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGGTGAGCTGAAGTGTCTTTCT
genomic: ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
EST: gi|86887181|gb|CI325996.1|CI325996
EST:     GATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
genomic: GATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
EST: gi|29666578|gb|CB662853.1|CB662853
EST:     ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
genomic: ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
EST: gi|33678849|gb|CF307088.1|CF307088
EST:     ACTTTGCGCATAAAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
genomic: ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
EST: gi|29632972|gb|CB637981.1|CB637981
EST:     ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
genomic: ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
EST: gi|29628141|gb|CB633152.1|CB633152
EST:     ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGGTGAGCTGAAGTGTCTTTCT
genomic: ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
EST: gi|86866749|gb|CI343555.1|CI343555
EST:     ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAG                         GAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT
genomic: ACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCT

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: 71 (upstream exon), 73 (downstream exon)
Score: 14

AAAACTGAAAGAAAAGGAACATGCTGTTCAATTGGAAAATTTAACCAAGAACTTTGCGCATACAACCAATTTGGATGTAACCTAATCTTGGAAAATGCAGgtatgctgtt ... tgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCTGAGCTGATGAGCTTTTTCTCAAAGTATCACGATTAAACCACAACAAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgatttgaacatggaagaagtgtgcataattgttttaccattgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCTGAGCTGATGAGCTTTTTCTCAAAGTATCACGATTAAACCACAACAAGAT
                                            ttgcctt  CT-rich tract
                             ataattgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgttacaaaaatcttgaaaacccctgctttacaattgagatgcattatacttttcatagccagtctacaaattctacctggtttatctgatccatgttggtagttgggtccttttattaattgatttgaacatggaagaagtgtgcataattgttttaccattgccttgtagGAACTGACATCAATCTGATGAAGTAGGACAGATGAGCTGAAGTGTCTTTCTGAGCTGATGAGCTTTTTCTCAAAGTATCACGATTAAACCACAACAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT