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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGATTTCTTGCTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgtttacatattgctctgtctaattattcctactctcataatcttcaccag

Basic information

species Oryza sativa
transcript LOC_Os07g49270.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 10
GCCGATTTCTTGCTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttctttctttctttaccaatctcatatttg-------tgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgt--ttacatattgctctg-------tctaattattcctactctca-taatcttcaccag
| || || ||||||||  |||||||||||||||||||||| |||||||||||||||||||||||   |  ||||||| | ||   | |  ||  ||       |  |||||     |  |  | ||     | ||  || | |   ||| |   ||   |||  |||         | || || |  | ||  || |   ||| | |||
GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcag

upper sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 5'ss of exon 10
GCCGATTTCTTGCTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttctttctttctttaccaatctcatatttgtgattctt-taaggtggtgttgttcgctatttgtcatgtaacacattgtttacatattgctctgtctaattattcctactctcataatcttcaccag
| || ||  | || || |||||  |  |||| |||||||||||| ||||||||||||||||||| |       |  |   |     |   |  | ||| || |    || |  || || | || | |||  || |  ||   | ||| || |||    |   | |                            
GTCGCTTCTTAGCAGAGTTGACTCATCAAGTTTTTTCTGATCTTAAAGCAAGTAAATATCAGgt-cagtgcaataccgaaagaggccatgttgtcgtggttttaacgagctattggtgattgccacttgggat-tcgcatggt-ttttcaaattttcatcattga----------------------------
















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|58696016|gb|CK084703.1|CK084703
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|29671780|gb|CB668055.1|CB668055
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|88577196|gb|CI673756.1|CI673756
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|29663749|gb|CB660024.1|CB660024
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|58686177|gb|CK074864.1|CK074864
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|33793650|gb|CF322709.1|CF322709
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|33679011|gb|CF307250.1|CF307250
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|88579491|gb|CI688488.1|CI688488
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|66924401|gb|CX111249.1|CX111249
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAA                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT

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: 62 (upstream exon), 59 (downstream exon)
Score: 24

GCCGATTTCTTGCTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGATTTCTTGCTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgtttacatattgctctgtctaattattcctactctcataatcttcaccag

- - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - AAGAAG
- - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - AGCAAG