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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

Basic information

species Oryza sativa
transcript LOC_Os04g59040.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 6
gtatatttt-ctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
|||| |  |  ||| | ||| ||||| | | |||||| |  |       | | ||      || |  |||||| |    |        | ||||   ||||   |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||
gtatttcatgttacagctctatttgtggtagagggaatagaa-------gagctc---tgcttcgacttgtttctaaccttggatttctgttgggcgttgt---cagGGTGAAAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCACTACAACGACATCAGCGAGCTGTCTCCTCACCGCCTGCAAGAGA

upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
gtatattttctactg--ttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
   |||||    ||     || ||||  | | ||||||||  |       |  || |||||    ||||     | |   ||       | ||||   ||||   |||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||
--gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactct----gtttcaaactatggctatc-----tgttgggcgttgt---cagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA

upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
||||||| |||     |   | | ||||  |   |||||    || |       | | | ||       |||      ||   |   | |   ||| ||  | ||||| ||||||||||| || || || |||||||||||||||||||| |||||    || || | |||| |||  || ||  | ||||| ||||||   ||||
gtatattctct-----tggctctttagctgataaaaaaa---ttgaa-------attttgttccaaccatttaaacaataacaagcttgtccaattgtgaca-cagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA

upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgtttt-----ttttttactgacgatattggatttt-------gtgatc--agGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
||| |   |  |||       |   |  |    |         |       |  | || ||| | |  ||||      | || ||||  | || ||| |||||       || ||   ||||||| || ||||||||||| || ||||| |||| |||||||||||||||    || |||| ||||||||  || ||  |||||||||| |||   || |
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactc-caatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA

upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
||| |  | |||   ||  |||| |  ||            | |   |  |||           | | | |  || |||      | | |||| |    | |  ||||||| || ||||||||||| || ||||| |||| |||||||||||| ||    ||   || | |||||| ||| ||  ||||||| || ||    || |
gta-acatcctaagctttagttttt--catgtttccttgtgctt---caagtttgtgtaaccattgtagctaattctttgg----ggttttggttgaaataa--agGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA

upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 4
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
                                                  |   | | |||   || | ||     |||    | ||   |    | | ||||||||| |||||||| || ||||| |||||||| || ||||||||||| || |||   |||| ||  |||||||   ||||  | |||||| | ||   |||||
-----------------------------------------------gtagcaaagtgtttacattcttttcagcgtttctctaagagtgtcatctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCAGAGA

upper sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 5
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
                                                  |   | | |||   |  | ||     |||    | ||   |    | | ||||||||| |||||||| || ||||| |||||||| || ||||||||||| || |||   |||| ||  |||||||   ||||  | |||||| | ||    ||||
-----------------------------------------------gtagcaaaatgtttacatccttttcagcgtttttctaagagtgtcatctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCGGAGA

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|86417243|gb|CI031452.1|CI031452
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|86498205|gb|CI140838.1|CI140838
EST:     GAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|33794379|gb|CF323075.1|CF323075
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|88217144|gb|CI216993.1|CI216993
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|33681023|gb|CF309262.1|CF309262
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|88985582|gb|CI016291.1|CI016291
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|86523613|gb|CI163819.1|CI163819
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|89171018|gb|CI040295.1|CI040295
EST:     AGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: AGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|86873424|gb|CI341649.1|CI341649
EST:     CCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: CCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|33686066|gb|CF314305.1|CF314305
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTG
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTG
EST: gi|58602895|gb|CK013423.1|CK013423
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|33681024|gb|CF309263.1|CF309263
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|66915284|gb|CX102132.1|CX102132
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGAGCAG                         AGTGAGAAGGATGACCAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|58603027|gb|CK013555.1|CK013555
EST:     TTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: TTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|11026234|gb|AU162835.1|AU162835
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|27554006|gb|CA997906.1|CA997906
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|55433023|gb|CV729535.1|CV729535
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGA
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGA
EST: gi|163918341|gb|EG713193.1|EG713193
EST:     TTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCTCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: TTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGC-CCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|32948454|gb|BP185026.1|BP185026
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTG
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTG
EST: gi|218494174|gb|FG955165.1|FG955165
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|87007333|gb|CI279004.1|CI279004
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|33693190|gb|CF321429.1|CF321429
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|58671895|gb|CK060581.1|CK060581
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|8527453|gb|AU092268.1|AU092268
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|86834579|gb|CI340696.1|CI340696
EST:     GAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|3768325|gb|AU032352.1|AU032352
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCNTGATTGACCAG                         GGTGAGANGGATGNCAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|86527296|gb|CI167502.1|CI167502
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|88984409|gb|CI014964.1|CI014964
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST: gi|55434349|gb|CV730296.1|CV730296
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCA
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCA
EST: gi|86846050|gb|CI347237.1|CI347237
EST:     ATGATTGAGCCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATA
genomic: ATGATTGA-CCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATA
EST: gi|86421029|gb|CI057018.1|CI057018
EST:     GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 29 (downstream exon)
Score: 108

GAGCCTGTTATTCCTGGTTCCTTCCTCCGTGCTAGAGCAATTGGCCTTATGCCCATGATTGACCAGgtatattttc ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
                           tactgac  putative branch site (score: 108)
     tctttttgttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA