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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcccttcacttaggatatttgggtgttctttctgtctggaagaagtagtgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG

Basic information

species Oryza sativa
transcript LOC_Os08g44400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G804772_T03 (Zea mays), 3'ss of exon 5
tttcccttcacttaggatattt--gggtgttctttctgtctggaagaagtagt--gtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG------------------------------
       |||  |  | | |     |   |   ||  ||   |||     | |  ||   |||| |  || || |   | |  |||| | | | | |  ||||||| ||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | |||||                              
----tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGGTGTGTATTCAACACATCTCCTTTTCACTT

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G825090_T05 (Zea mays), 3'ss of exon 5
-----tttcccttcacttaggatatttgggtgttctttctgtctggaagaagtagtgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG
     | |   ||  |  | || ||     ||     |        ||  |||  |     |||| |  ||| | |   | |  |||| | | | | |  ||||||| ||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | |||||
ggtcttctgagttttcccaagaaataaaattgcgtaatgaaatgcaaatcagttct-----atcattcagttataacagttacataagatgcacctctattgcagGTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G022866_T02 (Zea mays), 3'ss of exon 5
tttcccttcacttaggatattt--gggtgttctttctgtctggaagaagtagt--gtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG
       |||  |  | | |     |   |   ||  ||   |||     | |  ||   |||| |  || || |   | |  |||| | | | | |  ||||||||||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | |||||
----tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G085000_T03 (Zea mays), 3'ss of exon 4
tttcccttcacttaggatatttgggtgttctttctgtctggaagaagtag-tgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG
       |||  |  ||| |   |          ||  ||    ||| |  |  |    |||| ||| || |   | || |||| |||   | |  ||||||||||||||||||| ||||| |||||||||||||| |||| ||||||||||||||| || |||| |||||
-cgggtgtcatctgagatttcccgagaaataaattgcgtgatgaaagcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G022866_T01 (Zea mays), 3'ss of exon 5
tttcccttcacttaggatattt--gggtgttctttctgtctggaagaagtagt--gtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG------------------------------
       |||  |  | | |     |   |   ||  ||   |||     | |  ||   |||| |  || || |   | |  |||| | | | | |  ||||||||||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | |||||                              
----tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGGTGTGTATTCAACACATCTCCTTTTCACTT

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G825090_T03 (Zea mays), 3'ss of exon 5
tttcccttcacttaggatattt--gggtgttctttctgtctggaagaagtagt--gtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG
       |||  |  | | |     |   |   ||  ||   |||     | |  ||   |||| |  || || |   | |  |||| | | | | |  ||||||| ||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | |||||
----tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatcattcagtgttaacagttacataagatgcacctctattgcagGTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
----tttcccttcacttaggatatttgggt--gttctttctgtctggaagaagtagtgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG
    | ||     || |      ||||| |     |||  | |    |||  || | ||  || ||| |  |     |||  || |    |  |  || | |||||||||||||||||||||| ||||| ||||||||||| |||| ||| || || ||  |||  |  |||||||
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggt-gcgtccaaacaggtgctaagcttcaaaattt----tgtttctaag-tgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG

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|55408882|gb|CV721258.1|CV721258
EST:     AATTTCCTTACATG                         GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: AATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
EST: gi|58590549|gb|CF988857.1|CF988857
EST:     TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATG                         GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
EST: gi|29687876|gb|CB684151.1|CB684151
EST:     TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATG                         GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
EST: gi|58593409|gb|CF991717.1|CF991717
EST:     TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAAGGTCCTTACATG                         GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
EST: gi|27548923|gb|CA767585.2|CA767585
EST:     TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATG                         GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
EST: gi|29685102|gb|CB681377.1|CB681377
EST:     TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATG                         GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagtgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG
                                       tactctt  CT-rich tract
                tttgtttttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcccttcacttaggatatttgggtgttctttctgtctggaagaagtagtgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG

- -cccttca
- - - - - - - - - - - - -tgttctt
- - - - - - - - - - - - - - - - - tgtctgg
- - - - - - - - - - - - - - - - - - - - -aagaagta