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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

Basic information

species Oryza sativa
transcript LOC_Os06g04270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
||||||  |||   ||   |  |   | |           |  ||||    |  ||| |     ||| |||| |||||| | | |||||  | | || ||| ||||||||||||||||| || ||||| |||||| |||| ||||||||||||||||||||||| || ||||||||||| ||||| ||||| || || ||
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggtt--gctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
||  |   | |||      | | ||   ||  |||   |  |  || |   |          |||  |  |   | || |  |   |||| |||   |||| |||||||||||||| ||||| ||||| |||||  | || || |||||||||||| ||||||| || || |||||||| ||||  ||||||||||| ||
gttagatgtttcatt---ggtttatgttactgttatcatggtgagcctttttg---------ctgtgttctgttgcttatcctcacgttttgtt---tagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
|| ||  || | |  |  || |  ||  |      |||   | |  ||   |         | ||  | |||   | ||   | | | |   || |||||| |||||||||||||| ||||| ||||| |||||  |||||||||| ||||||||| |||||||  | | ||||||||| ||||  ||||||||||| ||
gtttg--atatgagttagagtttgtataatagaatagtaattctttttattttttatttttattgtttatttatttatccattattgctat-ttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaac-tgaatgtttcggtttcttgtttggtttcgt----tctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
                     | | |       | ||||| | |  |||    ||||  || | |   || |  |   | ||| ||    ||||    | | |||| |||||||||||||| ||||| ||||| |||||| | || || |||||||| ||| ||||||| || || |||||||| ||||  ||||||||||| ||
--------------------gttagatatttcattagtttatgttattgttatcatagtgagcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttc---tgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
          | |  |  |  |  |    | | |   ||| | || || | |  ||   || ||   |||         ||| |||  || |      || ||| |||||||| || |||||||||||||| |||||  | || ||||| ||||||||  |||||||| | || ||||| || ||||  ||||||||||| ||
---------gttagttagattttctc-tgcttct---tttgtgtgttttagttgatgttgatcttt-tgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
          |   |||  | || | | | ||| |   ||| |||  || ||   || |   || |||     |   |  ||| |  || | || | |||| |||||||||||||||||||| ||||| |||||  |||||  ||  ||||||||  |||||||  | |||||||| || ||||  |||||||| || ||
---------gttggctgctgttccttgaaacttaa---ttcaatgtctgtatgt-tagaatgct-aataaccggtccttatgtgttattgc-ttttatagGCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGTTTGGCCGCTGTGGAGAAGCATTTGGCTGCAAGATTCAACAAACCTGACAATGAGATTGTCGACCA

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttg-aatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
||  |          ||||  | | | |   |||   |    |  | |  || | |  |     ||    | | ||    |  |    |  | || |||||| |||||||||||||||||||| ||||| |||||  |||| ||||| |||| |||| |||||||||| |||||||| || ||||  ||||||||||||||
gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatcct----tccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA

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|29628849|gb|CB633860.1|CB633860
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29616150|gb|CB621162.1|CB621162
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58665775|gb|CK054461.1|CK054461
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58605211|gb|CK033244.1|CK033244
EST:     TCCAGGCCATCCCGAGAAGTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58694852|gb|CK083539.1|CK083539
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|38471630|gb|CF955761.1|CF955761
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|13420644|gb|AU174734.1|AU174734
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58608980|gb|CK037013.1|CK037013
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAA-TT-CCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29658985|gb|CB655260.1|CB655260
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|88316981|gb|CI625618.1|CI625618
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58693155|gb|CK081842.1|CK081842
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58611195|gb|CK038907.1|CK038907
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTCGGCTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAG
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGG-TCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAG
EST: gi|58607338|gb|CK035371.1|CK035371
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GAGCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29624781|gb|CB629792.1|CB629792
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|44679342|gb|CR292776.1|CR292776
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGTGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29621963|gb|CB626974.1|CB626974
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29627380|gb|CB632391.1|CB632391
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58610004|gb|CK038037.1|CK038037
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58612824|gb|CK040536.1|CK040536
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGG
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGG
EST: gi|38469502|gb|CF953633.1|CF953633
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29614101|gb|CB619114.1|CB619114
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29616061|gb|CB621073.1|CB621073
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|300215739|gb|HO088365.1|HO088365
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29658871|gb|CB655146.1|CB655146
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|29658330|gb|CB654605.1|CB654605
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58674058|gb|CK062744.1|CK062744
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|58586544|gb|CF984852.1|CF984852
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTTGCAAATGCAGTTGGGCTGGCCCTTGCTGAG
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATT-GCAAATGCAGTTGGGCTGGCCCTTGCTGAG
EST: gi|58670081|gb|CK058767.1|CK058767
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG                         GACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGA
EST: gi|88299800|gb|CI577302.1|CI577302
EST:     TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTAC-ACTG                         GACCTCT-GGTC
genomic: TCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTC

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: 75 (upstream exon), 75 (downstream exon)
Score: 73

GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatc ... cgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
                                          tttcgttct  CT-rich tract
     atacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT