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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatccagtccatacaacttgctccatttctttcttcctccacttactttttttctactggatctccaatcaccgaattaatgaaaatattgggtgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAGGATTTTGGTTCATTTGAGGCACTTGTAAAGAAGATGAGTGCAGAAGGTG

Basic information

species Oryza sativa
transcript LOC_Os05g25850.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g25850.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G124455_T01 (Zea mays), 3'ss of exon 2
gtaattatccagtccatacaacttgctccatttctttcttcctccacttactttttttctactggatctccaatcaccgaattaatgaaaatattgggtgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAGGATTTTGGTTCATTTGAGGCACTTGTAAAGAAGATGAGTGCAGAAGGTG
|||| ||||  ||  | ||||  || |   ||||     |  | |  || | |||||| |   |  |     |      || |  ||   ||||||| || ||| ||||| |||||||| || || |||||||  ||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||| ||||||||| |
gtaagtatcttgttaagacaatatgtt--gtttcaactgtgtttc-ttttccttttttgtgtcgttttctgga------aaattgtgtggatattggatgctttgcagGAAGGTGGTGGGGAGCCGCCACATGGGAAACTTGGCTGGGCCATCGATGAGGATTTTGGTTCATTTGAGGCACTTGTAAAGAGGATGAATGCAGAAGGCG

upper sequence: LOC_Os05g25850.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G059991_T01 (Zea mays), 3'ss of exon 2
gtaattatccagtccatacaacttgctccatttctttcttcctccacttactttttttctactggatctccaatcaccgaattaatgaaaatattgggtgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAGGATTTTGGTTCATTTGAGGCACTTGTAAAGAAGATGAGTGCAGAAGGTG
|| | | ||  ||  | |||| ||| |   ||||     | ||    |||  ||||||    | | | |          || | |||   ||||||  || ||| ||||| ||||| || || || || ||||  ||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||| ||||||||| |
gtgagtgtcttgttaagacaatttgtt--gtttcaactgtgcttg--ttatctttttttatgtcgctttatgg-----aaaattatgtggatattgaatgctttgcagGAAGGTGGCGGGGAGCCGCCTCATGGGAAACTTGGCTGGGCCATCGATGAGGATTTTGGTTCGTTTGAGGCACTTGTAAAGAAGATGAATGCAGAAGGCG
















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|88355464|gb|CI679182.1|CI679182
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGC                         GAGGGTGGTGGTGATCCACCA
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCACCA
EST: gi|1632331|gb|C20060.1|C20060
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAACCTNAAGCCTATCAGC                         GAGGGTGGTGGTGATCCACCACAATGCAAAACTT
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCACCACA-TGCAAAACTT
EST: gi|88378960|gb|CI681785.1|CI681785
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGC                         GAGGGTGGTGGTGATCCAC
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCAC
EST: gi|88364015|gb|CI610359.1|CI610359
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGC                         GAGGGTGGTGGTGATCCACCAC
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCACCAC
EST: gi|88760673|gb|CI770229.1|CI770229
EST:     GCCATGTCAATCATTCGATCTTCTGGAATACCCTCAAGCCTATCAGC                         GAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCCTTGATGAG
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAG
EST: gi|88569449|gb|CI660624.1|CI660624
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGC                         GAGGGTGGTGGTG
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTG
EST: gi|88334258|gb|CI642503.1|CI642503
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAAC-TCAAGCCTATCAGC                         GAGGGTGGTGGTGATCCACCACATG
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCACCACATG
EST: gi|88573928|gb|CI665697.1|CI665697
EST:     GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGC                         GAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAG
genomic: GCCATGTCAATCATTCGATCTTCTGGAATAACCTCAAGCCTATCAGCgtaattatcc ... tgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctactggatctccaatcaccgaattaatgaaaatattgggtgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAGGATTTTGGTTCATTTGAGGCACTTGTAAAGAAGATGAGTGCAGAAGGTG
                          aattaat  putative branch site (score: 3)
                          aattaatgaaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatccagtccatacaacttgctccatttctttcttcctccacttactttttttctactggatctccaatcaccgaattaatgaaaatattgggtgttttacagGAGGGTGGTGGTGATCCACCACATGCAAAACTTGGCTGGGCCATTGATGAGGATTTTGGTTCATTTGAGGCACTTGTAAAGAAGATGAGTGCAGAAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG