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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtctgtcctttaagctctctggtgcccttttatggatctaattttcgtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 25
---------------------------------------------------gtaagtgtctgtcctttaagctct---ctggtgccctttta-tggatctaattttcgtcatgta---cagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                                                    |  || || |   ||| | || |    || |||      | |||| ||  |||   |  |||    ||||||  |||||||||||||||||||||| || || ||||| || |||||||||
gtaagtgccccctctttttttccctggacccgaagggttagagaaggaaggatgggtttcaggtgttttatctatggtttgttgcatgacgaatggaacttgtttctttggtgtgaaccagGATCAGAGATGATTTTGAGAAAGAGGACGCGTTTCATGGACTGTGTGCAATG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 25
---------------------------------gtaagtgtctgtcctttaagctctctggtgcccttttatg--gatctaattttc----gtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                                  ||  ||||     ||| |  |  |||||   ||| |||    ||||   |||     ||  | | |||||||||||||||| |||||||||||||||| ||    ||||||||||| |||
atctcaacatcactttacaaattgaccataatattagatgtccactgtttca--ttgctggttatcttgtatattaatctctctttgatgggttttttgcagGATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 25
----------------------------------gtaagtgtctgtcctttaagctctctggtgcccttttatg--gatctaattttcgtcatgt---acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                                   ||  ||||     ||| |  |  |||||   ||| |||    || |   |||  | || |    |||||||||||||||| |||||||||||||||| ||    ||||||||||| |||
ctcaacctcttcactttacaaattgatcataatattagatgtccactgtttca--ttgctggttatcttgtatattaatttctctttgatgattttttgcagGATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 25
----------------------------gtaagtgtctgtcctttaagctct--ctggtgcccttttatggatctaat--tttcgtcatgt-----acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                              |    | || |   | ||| |   |   | |  |||||    |  | |  |  |  || ||      ||||||||| |||||| ||||||| || ||||| |||| ||||||||||||||  
attggactcatactaccttttacatatgccataactttgcctgctgagcacaggcccattcttttttaacagttcattaataccaacaagttcatggcagGATACGTGATGATATTGAGAAGGAAGATGCCTTCCGTGGTCTATGTGCAACT

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 3'ss of exon 25
--------------------------------gtaagtgtctgtcctttaa--gctctctggtgccc-ttttatggatctaattttcgtcatgtac--agGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                                    |  | |  | ||| |  | ||| | ||  |  |||||     ||| ||||  |  | | |  |||||||||||||||||||||||||| ||||| || |  || || ||||| |||
gtatctattttgttacttgttcaatctcttcaacttggttttaccgtttgatcgttctttcgtatcagttttaaactactattttttcttttcttctcagGATACGAGATGATTTTGAGAAAGAAGATGCTTTTCGAGGCCTGTGTGCTATG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S41_175V6.1 (Physcomitrella patens), 3'ss of exon 24
------------------------------gtaagtgtc-tgtcctttaagctctctggtgccctt--ttatg--gatctaattttcgtcatg--tacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                              ||  || |  ||    | |||   || |   |  ||  | |||  |  || |  |   || ||  | |||||||||||||||||||||||| || ||||||||||  ||  | ||||| |||
gtttttgaggttgtgtttgaggttgtttgcgtttgtatgatgataatgaagaagtcagtcccttttactcatgatgcactgaaatatatcttgcttgcagGATACGAGATGATTTTGAGAAGGAAGATGCATTCCGGGGCTTGTGTGCCATG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
----------------------------------gtaagtgtctgtcctttaagctctctggtgccc--ttttatggatctaattttcgtcatgt-acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                                   |  || |||    | |  | | | |  |      ||| |   |   | ||||  ||   | ||||||||||||||||||||||||| || ||||| || |  ||  | ||||| |||
tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG

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|58608072|gb|CK036105.1|CK036105
EST:     GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCAT                         GATACGAGATGATTTTGAGAA
genomic: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAA
EST: gi|58592654|gb|CF990962.1|CF990962
EST:     GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCAT                         GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
genomic: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcctttaagctctctggtgcccttttatggatctaattttcgtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
                                 atctaat  putative branch site (score: 3)
                                       ttttcgtc  CT-rich tract
                                 atctaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtctgtcctttaagctctctggtgcccttttatggatctaattttcgtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG