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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATCAAGGGGAGGATTAACAGGGCTGTATGGGGGCCGTTGAACAGGACCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgcatttacaacatttgcacatagttctactaaccatcgttggtgctacaaactcatcgctagtactaggcttctggtgcttttcaggaatgc...

Basic information

species Oryza sativa
transcript LOC_Os05g16660.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G028834_T03 (Zea mays), 5'ss of exon 2
TGGCATCAAGGGGAGGATTAACAGGGCTGTATGGGGGCCGTTGAACAGGACCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttag-----cttgcatttacaacatttgcacatagttctactaaccatcgttggtgctacaaactcatcgctagtactaggcttctggtgcttttcaggaatgc
 ||||||||||| ||||| |||||||| || ||||| ||| ||||||||||||| ||||| ||||| |||||||||||||| ||||| |||||| | ||||| ||     | |||   || |  |  | ||  ||||||| ||||  ||   |     | |         |  |   | | | | | |  |    | |  |    
CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGCCCGCTGAACAGGACCATTATCACTGCCGGGGAGGATGCCACCATTCGCATCTGGGACTCAGAGgtcaggatatcatgctgatagagtaactcca-gtagttct-ctaatgatgtctttgattgcgggacagctgggacagccacgttcccgtcgtcccttatcat---

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 2
TGGCATCAAGGGGAGGATTAACAGGGCTGTATGGGGGCCGTTGAACAGGACCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgcatttacaacatttgcacatagt-tctactaaccatcg-----ttggtgctacaaactcatcgctagtactaggcttctggtgcttttcaggaatgc
 ||||||||||| ||||| |||||||| || ||||||||| | ||||||||||||||||| ||||| |||||||||||| | |||||||||||  | ||||||||  |||  |  |  ||  |     | || || ||||    | |      | |  |||  ||  |  |   |||     | |  |   |   |   ||     
CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc--tggctgcagataggactggtgtccactataatttggttatctagccctaagaatgccccatcagttgcttgttgttacggggctatgggc----
















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|25797590|gb|CA753551.1|CA753551
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|66924182|gb|CX111030.1|CX111030
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88267414|gb|CI379349.1|CI379349
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88688380|gb|CI731956.1|CI731956
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88688391|gb|CI731967.1|CI731967
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88688679|gb|CI732255.1|CI732255
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88690961|gb|CI735040.1|CI735040
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88690662|gb|CI734741.1|CI734741
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88691102|gb|CI735181.1|CI735181
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|55411136|gb|CV723512.1|CV723512
EST:     CCATCATCACCGCCGGTGAGGATTCTTTCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
EST: gi|88691159|gb|CI735238.1|CI735238
EST:     CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAG                         ACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA
genomic: CCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgc ... gcatgtgcagACTGGAACATGTCTGAATGAGTCAGACAAAGAACAAGGACACCAGAAAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCATCAAGGGGAGGATTAACAGGGCTGTATGGGGGCCGTTGAACAGGACCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgcatttacaacatttgcacatagttctactaaccatcgttggtgctacaaactcatcgctagtactaggcttctggtgcttttcaggaatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG