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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT

Basic information

species Oryza sativa
transcript LOC_Os11g39220.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G419782_T01 (Zea mays), 3'ss of exon 2
------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
       |  || |   ||    |||||   |   |  |||        || | | |  || |   ||  |  |    | || | ||    ||  |||   || |||||| |||||||| |||||||||||||| |||||||| ||||  || ||||||||||||||||| || || || ||||||||||||||||||||||||||
caatgtctcaatactgttgtgttctgtttattttga--atggcgcacagtagggcttgtacccagcacc-taacgcactgttgtgtt---cttttcttgcaaatagGATCGAATGTCCAAGCCCTACAAACTACCGCTACATTTGATCATGTCACTGATGAGTTCATTATTAACACCCCAAATGATGGAGCTATTAAGTGGTGGAT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G445791_T01 (Zea mays), 3'ss of exon 2
------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
       |  || |   ||    |||||   |   |  |||        || | | |  || |   ||  |  |    | || | ||    ||  |||   || |||||| |||||||| |||||||||||||| |||||||| ||||  || ||||||||||||||||| || || || ||||||||||||||||||||||||||
cagtgtctcaatactgttgtgttctgtttattttga--atggcgcacagtagggcttgtacccagcacc-taacgcactgttgtgtt---cttttcttgcaaatagGATCGAATGTCCAAGCCCTACAAACTACCGCTACATTTGATCATGTCACTGATGAGTTCATTATTAACACCCCAAATGATGGAGCTATTAAGTGGTGGAT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G445791_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
                                                                                                   |  || |   ||    |||||   |   |  |||        || | | |  || |   ||  |  |    | || | ||    ||  |||   || |||||| |||||||| |||||||||||||| |||||||| ||||  || ||||||||||||||||| || || || ||||||||||||||||||||||||||
gttaggttctccacttatatttatttattatccaataattggtgctgtctctattattttgcttagcactttatcaatgtacagtccagctacagtgtctcaatactgttgtgttctgtttattttga--atggcgcacagtagggcttgtacccagcacc-taacgcactgttgtgtt---cttttcttgcaaatagGATCGAATGTCCAAGCCCTACAAACTACCGCTACATTTGATCATGTCACTGATGAGTTCATTATTAACACCCCAAATGATGGAGCTATTAAGTGGTGGAT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G820287_T02 (Zea mays), 3'ss of exon 2
------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
       |  || |   ||    |||||   |   |  |||        || | | |  || |   ||  |  |    | || | ||    ||  |||   || |||||| |||||||| |||||||||||||| |||||||| ||||  |||||||||||||||||||| || || || ||||||||||||||||||||||||||
cagtgtctcaatactgttgtgttctgtttattttga--atggcgcacagtagggcttgtacccagcacc-taacgcactgttgtgtt---cttttcttgcaaatagGATCGAATGTCCAAGCCCTACAAACTACCGCTACATTTGATCATGTTACTGATGAGTTCATTATTAACACCCCAAATGATGGAGCTATTAAGTGGTGGAT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G045376_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
                                                                                                   |  || |   ||    |||||   |   |  |||        || | | |  || |   ||    | |    || || | | | ||  |||   || |||||| |||||||| |||||||||||||| |||||||| ||||| || ||||||||||||||||| || || || ||||||||||||||||||||||||||
gttaggttctccacttatatttatttattatccaataattggtgctatctctattattttgcttagcactttatcaatgtacagtccagctacagtgtctcaatactgttgtgttctgtttattttga--atggcgcacagtagggcttgtacccagcac---ctaacgcaatgttgtgt-tcttttcttgcaaatagGATCAAATGTCCAAGCCCTACAAACTACCGCTACATTTGATCCTGTCACTGATGAGTTCATTATTAACACCCCAAATGATGGAGCTATTAAGTGGTGGAT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G099666_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
                                                                                                   |  || |   ||    |||||   |   |  |||  |     || | | |  || |   ||  |  |    | || | ||    ||  ||    || |||||| |||||||| |||||||| ||||| |||||||| ||||| || ||||||||||||||||| || || || ||||||||||||||||||||||||||
gttaggttctccacttatatttatttattatccaataattggtgctgtctctattattttgcttagcaatttatcaatgtacagtgcagctacagtgtctcaatactgttgtgttctgtttattttga--atggcacacagtagggcttgtacccagcacc-taacgcactgttgtgtt---cttttctcgcaaatagGATCGAATGTCCAAGCCCTACAGACTACCGCTACATTTGATCCTGTCACTGATGAGTTCATTATTAACACTCCAAATGATGGAGCTATTAAGTGGTGGAT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G419782_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------------attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
                                                                                                   |  || |   ||    |||||   |   |  |||        || | | |  || |   ||  |  |    | || | ||    ||  |||   || |||||| |||||||| |||||||||||||| |||||||| ||||  || ||||||||||||||||| || || || ||||||||||||||||||||||||||
gttaggttctccacttatatttatttattatccaataattggtgttgtctctattattttgcttagcactttatcaatgtacagtccagctacaatgtctcaatactgttgtgttctgtttattttga--atggcgcacagtagggcttgtacccagcacc-taacgcactgttgtgtt---cttttcttgcaaatagGATCGAATGTCCAAGCCCTACAAACTACCGCTACATTTGATCATGTCACTGATGAGTTCATTATTAACACCCCAAATGATGGAGCTATTAAGTGGTGGAT

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|29641782|gb|CB646789.1|CB646789
EST:     GAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
genomic: GAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
EST: gi|29678643|gb|CB674918.1|CB674918
EST:     CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
genomic: CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
EST: gi|58610022|gb|CK038055.1|CK038055
EST:     CGACAATTTGGATGATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAGACTACTGCTACATTCGATCCAGTTACTG
genomic: CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
EST: gi|29678050|gb|CB674325.1|CB674325
EST:     CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
genomic: CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT
                ctatttcatcttattt  CT-rich tract
             ttactatttcatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcatgcccatgcagcctgttagctcccatcatgataatagttaagtcctccacacgttactatttcatcttattttatttattttcccttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTGATGAGTTCATTATCAATACACCCAATGATGGAGCTATTAAGTGGTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA