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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggatggcaacatccagtaatattcatggtgcatagtactaaattattacaaacttttatgtccgttgttttgatgtccactataccatcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGCCCAGATGCCATCAAGACTTCCAGCGAAGCATTGGACACCTGCAACACTA

Basic information

species Oryza sativa
transcript LOC_Os02g07260.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G382914_T03 (Zea mays), 3'ss of exon 5
---tgtggatggcaacatccagtaatattcatggtgcatagtactaaattattacaaacttttatgtccgttgttttgatgtccactataccatcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGCCCAGATGCCATCAAGACTTCCAGCGAAGCATTGGACACCTGCAACACTA
   |||  || |  | ||    |  ||||  ||    |||||  |     | | ||       |      ||  |   |||   |||  |    | | | |||| |||  ||||| | |||||||| ||||  ||||||||||||||||||||||| ||||||| ||| || | |  ||||||||||||||||  ||| ||| 
cagtgttaatagtgatatgacatgttattt-tgtacgatagtttttccacagtgcagcaccggaaacaaatt--tgccatgctaacttgagtgacttctacagATTGTCCCTGCCACTGCTATCCCTGATGACTGGATGGGTCTTGATGTTGGCCCTGATGCCACCAAAACATTCGACGAAGCATTGGACACCACCAAGACTG

upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 4
-----tgtggatggcaacatccagtaatattcatgg----tgcatagtactaaattattacaaacttttatgtccgttgttttgatgtccac-tataccatcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGCCCAGATGCCATCAAGACTTCCAGCGAAGCATTGGACACCTGCAACACTA
     | |    | ||   |     | | |  ||||    || ||   | ||||  |||  || | | |      ||   ||| | |   ||  |||  | |  || ||||  ||  | ||| | || ||||| ||||| ||||||||||| ||| |||| |||||  |||||||||| | |||||||||  |||||||   ||| || |
gtaactatcacagtcattgtggttgactctcaatgggccatgtatgaaagtaaaacatt-taagcgtctggtctggtctctttaaagctgacacatatga-ctcttgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGTCCAGACTCCATCAAGACATTCAGCGAAGCTCTGGACACAACCAAAACCA
















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|33678660|gb|CF306899.1|CF306899
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGC
EST: gi|300216018|gb|HO088644.1|HO088644
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
EST: gi|29671336|gb|CB667611.1|CB667611
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
EST: gi|29614437|gb|CB619450.1|CB619450
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
EST: gi|33690622|gb|CF318861.1|CF318861
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTG
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTG
EST: gi|33795493|gb|CF323616.1|CF323616
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTTGATGTTGG
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTT-GATGTTGG
EST: gi|33805002|gb|CF328378.1|CF328378
EST:     CTACCGATGTTGTAGTGGCTCACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGC
EST: gi|117247218|gb|CT848558.1|CT848558
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTC
EST: gi|27554292|gb|CA998192.1|CA998192
EST:     CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAG                         ACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC
genomic: CTACCGATGTTGTAGTGGCTGACAAGTTTGCCGCAGATGCTGAAAGCAAGgtttgttcat ... tcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattacaaacttttatgtccgttgttttgatgtccactataccatcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGCCCAGATGCCATCAAGACTTCCAGCGAAGCATTGGACACCTGCAACACTA
                         ttttgat  putative branch site (score: 4)
                                             tcattttc  putative PPT
       aaacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggatggcaacatccagtaatattcatggtgcatagtactaaattattacaaacttttatgtccgttgttttgatgtccactataccatcattttcagACTGTTGCTGCCTCCGCTATCCCCGATGGTTGGATGGGTCTTGATGTTGGCCCAGATGCCATCAAGACTTCCAGCGAAGCATTGGACACCTGCAACACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG