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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttcccacctcatcgcttacttctgtttgatataccatcttgctaatataatcatccccatttcag

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 5
ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttcccacctcatcgcttacttct-----gtttgatataccatcttgctaatataatcatccccatttcag
|| ||||||||||||||||||||||| || ||||||||||||||  |||| ||    |  | |||||     ||  | | |||  || |||||||||    ||  | |||||||
ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAGgtatgctcacccaactttctgtgtgcttcttgtccgtgaggtttact-tcatgctaatatt-caataacaatttcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G141587_T01 (Zea mays), 5'ss of exon 5
ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttcccacctcatcgcttacttctgtt----tgatataccatcttgctaatataatcatccccatttcag
|| ||||||||||||||||||||||| || |||||||||||||    |||  |    |||| ||||| ||    |    |  |||| |||| ||||   |||  | |||||||
ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAGgtatgcacaaccaattttctgcttgcttctcttcccttaggtttacatcatgctgatatt-ccataacaatttcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 5
ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttcccacctcatcgcttact------tctgtttgatatacc---atcttgctaatataatcatccccatttcag--------------------------------------------------
|| ||||  ||||||||||||||||| || ||||||||||||       || | |||  || |       ||| |||| | |      ||     | ||  | |  | | || ||                                                     
ACAATGGCAAAATCATTTGAAGTCACTGAATTACCAGgtatgtacatgtactttatctgtttccatatgctctatttggtgtgattgaattcccttgatccatttttactcaatttctctcttattggtaaggttattacatgtttcaattttacattatcattgcag

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|58661505|gb|CK050185.1|CK050185
EST:     GCAGACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCGCACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: GCAGACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|29613909|gb|CB618922.1|CB618922
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCGCACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|88349632|gb|CI632767.1|CI632767
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCACACGGAA
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAA
EST: gi|88348222|gb|CI637683.1|CI637683
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCACACGG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGG
EST: gi|58685502|gb|CK074189.1|CK074189
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCGCACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|58601041|gb|CK011569.1|CK011569
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCGCACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|29680636|gb|CB676911.1|CB676911
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|88575756|gb|CI669901.1|CI669901
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|3760098|gb|C97356.1|C97356
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
EST: gi|29671006|gb|CB667281.1|CB667281
EST:     ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAG                         TTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG
genomic: ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCG

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: 70 (upstream exon), 71 (downstream exon)
Score: 66

ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttc ... cccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCGACGATATGTTCATACGTGTGTACAATTACAATACGATGGATAAGGTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGATGGTGAAATCATTTGAAGTCACAGAGTTACCAGgtatgctttcccacctcatcgcttacttctgtttgatataccatcttgctaatataatcatccccatttcag

- - - - - - - - TTGAAG